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Zappa S, Berne C, Morton Iii RI, Whitfield GB, De Stercke J, Brun YV. The HmrABCX pathway regulates the transition between motile and sessile lifestyles in Caulobacter crescentus by a mechanism independent of hfiA transcription. mBio 2024:e0100224. [PMID: 39230277 DOI: 10.1128/mbio.01002-24] [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: 04/02/2024] [Accepted: 06/03/2024] [Indexed: 09/05/2024] Open
Abstract
During its cell cycle, the bacterium Caulobacter crescentus switches from a motile, free-living state, to a sessile surface-attached cell. During this coordinated process, cells undergo irreversible morphological changes, such as shedding of their polar flagellum and synthesis of an adhesive holdfast at the same pole. In this work, we used genetic screens to identify genes involved in the regulation of the transition from the motile to the sessile lifestyle. We identified a predicted hybrid histidine kinase that inhibits biofilm formation and promotes the motile lifestyle: HmrA (holdfast and motility regulator A). Genetic screens and genomic localization led to the identification of additional genes that form a putative phosphorelay pathway with HmrA. We postulate that the Hmr pathway acts as a rheostat to control the proportion of cells harboring a flagellum or a holdfast in the population. Further genetic analysis suggests that the Hmr pathway impacts c-di-GMP synthesis through the diguanylate cyclase DgcB pathway. Our results also indicate that the Hmr pathway is involved in the regulation of motile to sessile lifestyle transition as a function of various environmental factors: biofilm formation is repressed when excess copper is present and derepressed under non-optimal temperatures. Finally, we provide evidence that the Hmr pathway regulates motility and adhesion without modulating the transcription of the holdfast synthesis regulator HfiA. IMPORTANCE Complex communities attached to a surface, or biofilms, represent the major lifestyle of bacteria in the environment. Such a sessile state enables the inhabitants to be more resistant to adverse environmental conditions. Thus, having a deeper understanding of the underlying mechanisms that regulate the transition between the motile and the sessile states could help design strategies to improve biofilms when they are beneficial or impede them when they are detrimental. For Caulobacter crescentus motile cells, the transition to the sessile lifestyle is irreversible, and this decision is regulated at several levels. In this work, we describe a putative phosphorelay that promotes the motile lifestyle and inhibits biofilm formation, providing new insights into the control of adhesin production that leads to the formation of biofilms.
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Affiliation(s)
- Sébastien Zappa
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Quebec, Canada
| | - Cécile Berne
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Quebec, Canada
| | | | - Gregory B Whitfield
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Quebec, Canada
| | - Jonathan De Stercke
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Quebec, Canada
| | - Yves V Brun
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Quebec, Canada
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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2
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Frando A, Grundner C. More than two components: complexities in bacterial phosphosignaling. mSystems 2024; 9:e0028924. [PMID: 38591891 PMCID: PMC11097640 DOI: 10.1128/msystems.00289-24] [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] [Indexed: 04/10/2024] Open
Abstract
For over 40 years, the two-component systems (TCSs) have taken front and center in our thinking about the signaling mechanisms by which bacteria sense and respond to their environment. In contrast, phosphorylation on Ser/Thr and Tyr (O-phosphorylation) was long thought to be mostly restricted to eukaryotes and a somewhat accessory signaling mechanism in bacteria. Several recent studies exploring systems aspects of bacterial O-phosphorylation, however, now show that it is in fact pervasive, with some bacterial proteomes as highly phosphorylated as those of eukaryotes. Labile, non-canonical protein phosphorylation sites on Asp, Arg, and His are now also being identified in large numbers in bacteria and first cellular functions are discovered. Other phosphomodifications on Cys, Glu, and Lys remain largely unexplored. The surprising breadth and complexity of bacterial phosphosignaling reveals a vast signaling capacity, the full scope of which we may only now be beginning to understand but whose functions are likely to affect all aspects of bacterial physiology and pathogenesis.
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Affiliation(s)
- Andrew Frando
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Christoph Grundner
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
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3
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Zappa S, Berne C, Morton RI, De Stercke J, Brun YV. The HmrABCX pathway regulates the transition between motile and sessile lifestyles in Caulobacter crescentus by a HfiA-independent mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571505. [PMID: 38168291 PMCID: PMC10760086 DOI: 10.1101/2023.12.13.571505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Through its cell cycle, the bacterium Caulobacter crescentus switches from a motile, free-living state, to a sessile surface-attached cell. During this coordinated process, cells undergo irreversible morphological changes, such as shedding of their polar flagellum and synthesis of an adhesive holdfast at the same pole. In this work, we used genetic screens to identify genes involved in the regulation of the motile to sessile lifestyle transition. We identified a predicted hybrid histidine kinase that inhibits biofilm formation and activates the motile lifestyle: HmrA (Holdfast and motility regulator A). Genetic screens and genomic localization led to the identification of additional genes that regulate the proportion of cells harboring an active flagellum or a holdfast and that form a putative phosphorelay pathway with HmrA. Further genetic analysis indicates that the Hmr pathway is independent of the holdfast synthesis regulator HfiA and may impact c-di-GMP synthesis through the diguanylate cyclase DgcB pathway. Finally, we provide evidence that the Hmr pathway is involved in the regulation of sessile-to-motile lifestyle as a function of environmental stresses, namely excess copper and non-optimal temperatures.
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Affiliation(s)
- Sébastien Zappa
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec, CANADA
| | - Cecile Berne
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec, CANADA
| | - Robert I. Morton
- Department of Biology, Indiana University, Bloomington, IN, USA
- Present address: Boston Scientific, Yokneam, Northern, ISRAEL
| | - Jonathan De Stercke
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec, CANADA
- Present address: Unité de Recherche en Biologie des Micro-organismes, Université de Namur, 61 rue de Bruxelles, B-5000 Namur, BELGIUM
| | - Yves V. Brun
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec, CANADA
- Department of Biology, Indiana University, Bloomington, IN, USA
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4
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Hespanhol JT, Nóbrega-Silva L, Bayer-Santos E. Regulation of type VI secretion systems at the transcriptional, posttranscriptional and posttranslational level. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001376. [PMID: 37552221 PMCID: PMC10482370 DOI: 10.1099/mic.0.001376] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023]
Abstract
Bacteria live in complex polymicrobial communities and are constantly competing for resources. The type VI secretion system (T6SS) is a widespread antagonistic mechanism used by Gram-negative bacteria to gain an advantage over competitors. T6SSs translocate toxic effector proteins inside target prokaryotic cells in a contact-dependent manner. In addition, some T6SS effectors can be secreted extracellularly and contribute to the scavenging scarce metal ions. Bacteria deploy their T6SSs in different situations, categorizing these systems into offensive, defensive and exploitative. The great variety of bacterial species and environments occupied by such species reflect the complexity of regulatory signals and networks that control the expression and activation of the T6SSs. Such regulation is tightly controlled at the transcriptional, posttranscriptional and posttranslational level by abiotic (e.g. pH, iron) or biotic (e.g. quorum-sensing) cues. In this review, we provide an update on the current knowledge about the regulatory networks that modulate the expression and activity of T6SSs across several species, focusing on systems used for interbacterial competition.
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Affiliation(s)
- Julia Takuno Hespanhol
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-900, Brazil
| | - Luize Nóbrega-Silva
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-900, Brazil
| | - Ethel Bayer-Santos
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-900, Brazil
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5
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Gangwal A, Kumar N, Sangwan N, Dhasmana N, Dhawan U, Sajid A, Arora G, Singh Y. Giving a signal: how protein phosphorylation helps Bacillus navigate through different life stages. FEMS Microbiol Rev 2023; 47:fuad044. [PMID: 37533212 PMCID: PMC10465088 DOI: 10.1093/femsre/fuad044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/04/2023] Open
Abstract
Protein phosphorylation is a universal mechanism regulating a wide range of cellular responses across all domains of life. The antagonistic activities of kinases and phosphatases can orchestrate the life cycle of an organism. The availability of bacterial genome sequences, particularly Bacillus species, followed by proteomics and functional studies have aided in the identification of putative protein kinases and protein phosphatases, and their downstream substrates. Several studies have established the role of phosphorylation in different physiological states of Bacillus species as they pass through various life stages such as sporulation, germination, and biofilm formation. The most common phosphorylation sites in Bacillus proteins are histidine, aspartate, tyrosine, serine, threonine, and arginine residues. Protein phosphorylation can alter protein activity, structural conformation, and protein-protein interactions, ultimately affecting the downstream pathways. In this review, we summarize the knowledge available in the field of Bacillus signaling, with a focus on the role of protein phosphorylation in its physiological processes.
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Affiliation(s)
- Aakriti Gangwal
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
| | - Nishant Kumar
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
| | - Nitika Sangwan
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
- Department of Biomedical Science, Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi-110075, India
| | - Neha Dhasmana
- School of Medicine, New York University, 550 First Avenue New York-10016, New York, United States
| | - Uma Dhawan
- Department of Biomedical Science, Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi-110075, India
| | - Andaleeb Sajid
- 300 Cedar St, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, New Haven CT, United States
| | - Gunjan Arora
- 300 Cedar St, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, New Haven CT, United States
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
- Delhi School of Public Health, Institution of Eminence, University of Delhi, Delhi-110007, India
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Kumarapperuma I, Tom IP, Bandara S, Montano S, Yang X. Mode of autophosphorylation in bacteriophytochromes RpBphP2 and RpBphP3. Photochem Photobiol Sci 2023; 22:1257-1266. [PMID: 36757561 PMCID: PMC10619329 DOI: 10.1007/s43630-023-00366-9] [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: 11/29/2022] [Accepted: 01/12/2023] [Indexed: 02/10/2023]
Abstract
Phytochromes are red-light photoreceptors that regulate a wide range of physiological processes in plants, fungi and bacteria. Canonical bacteriophytochromes are photosensory histidine kinases that undergo light-dependent autophosphorylation, thereby regulating cellular responses to red light via two-component signaling pathways. However, the molecular mechanism of kinase activation remains elusive for bacteriophytochromes. In particular, the directionality of autophosphorylation is still an open question in these dimeric photoreceptor kinases. In this work, we perform histidine kinase assays on two tandem bacteriophytochromes RpBphP2 and RpBphP3 from the photosynthetic bacterium Rhodopseudomonas palustris. By examining the kinase activities of full-length bacteriophytochromes and two loss-of-function mutants under different light conditions, we demonstrate that RpBphP2 and RpBphP3 undergo light-dependent trans-phosphorylation between protomers in both homodimeric and heterodimeric forms. We have further determined the crystal structure of the histidine kinase domains of RpBphP2 at 3.19 Å resolution. Based on structural comparisons and homology modeling, we also present a model to account for the actions of trans-autophosphorylation in bacteriophytochromes.
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Affiliation(s)
| | - Irin P Tom
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | - Sepalika Bandara
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | - Sherwin Montano
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | - Xiaojing Yang
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA.
- Department of Ophthalmology and Vision Sciences, University of Illinois Chicago, Chicago, IL, USA.
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Wang L, Fan R, Li Z, Wang L, Bai X, Bu T, Dong Y, Xu Y, Quan C. Insights into the structure and function of the histidine kinase ComP from Bacillus amyloliquefaciens based on molecular modeling. Biosci Rep 2022; 42:BSR20220352. [PMID: 36052710 PMCID: PMC9620489 DOI: 10.1042/bsr20220352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 08/01/2022] [Accepted: 09/01/2022] [Indexed: 11/21/2022] Open
Abstract
The ComPA two-component signal transduction system (TCS) is essential in Bacillus spp. However, the molecular mechanism of the histidine kinase ComP remains unclear. Here, we predicted the structure of ComP from Bacillus amyloliquefaciens Q-426 (BaComP) using an artificial intelligence approach, analyzed the structural characteristics based on the molecular docking results and compared homologous proteins, and then investigated the biochemical properties of BaComP. We obtained a truncated ComPS protein with high purity and correct folding in solution based on the predicted structures. The expression and purification of BaComP proteins suggested that the subdomains in the cytoplasmic region influenced the expression and stability of the recombinant proteins. ComPS is a bifunctional enzyme that exhibits the activity of both histidine kinase and phosphotransferase. We found that His571 played an obligatory role in the autophosphorylation of BaComP based on the analysis of the structures and mutagenesis studies. The molecular docking results suggested that the HATPase_c domain contained an ATP-binding pocket, and the ATP molecule was coordinated by eight conserved residues from the N, G1, and G2 boxes. Our study provides novel insight into the histidine kinase BaComP and its homologous proteins.
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Affiliation(s)
- Lulu Wang
- School of Life Science and Biotechnology, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, Liaoning, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, China
| | - Ruochen Fan
- School of Life Science and Biotechnology, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, Liaoning, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, China
| | - Zhuting Li
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, China
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, Liaoning, China
| | - Lina Wang
- Institute of Cancer Stem Cell, Dalian Medical University, 9 Western Lvshun Road, Dalian 116044, Liaoning, China
| | - Xue Bai
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, China
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, Liaoning, China
| | - Tingting Bu
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, China
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, Liaoning, China
| | - Yuesheng Dong
- School of Life Science and Biotechnology, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, Liaoning, China
| | - Yongbin Xu
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, China
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, Liaoning, China
| | - Chunshan Quan
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, China
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, Liaoning, China
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8
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Krüger A, Frunzke J. A pseudokinase version of the histidine kinase ChrS promotes high heme tolerance of Corynebacterium glutamicum. Front Microbiol 2022; 13:997448. [PMID: 36160252 PMCID: PMC9491836 DOI: 10.3389/fmicb.2022.997448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/18/2022] [Indexed: 11/21/2022] Open
Abstract
Heme is an essential cofactor for almost all living cells by acting as prosthetic group for various proteins or serving as alternative iron source. However, elevated levels are highly toxic for cells. Several corynebacterial species employ two paralogous, heme-responsive two-component systems (TCS), ChrSA and HrrSA, to cope with heme stress and to maintain intracellular heme homeostasis. Significant cross-talk at the level of phosphorylation between these systems was previously demonstrated. In this study, we have performed a laboratory evolution experiment to adapt Corynebacterium glutamicum to increasing heme levels. Isolated strains showed a highly increased tolerance to heme growing at concentrations of up to 100 μM. The strain featuring the highest heme tolerance harbored a frameshift mutation in the catalytical and ATPase-domain (CA-domain) of the chrS gene, converting it into a catalytically-inactive pseudokinase (ChrS_CA-fs). Reintroduction of the respective mutation in the parental C. glutamicum strain confirmed high heme tolerance and showed a drastic upregulation of hrtBA encoding a heme export system, conserved in Firmicutes and Actinobacteria. The strain encoding the ChrS pseudokinase variant showed significantly higher heme tolerance than a strain lacking chrS. Mutational analysis revealed that induction of hrtBA in the evolved strain is solely mediated via the cross-phosphorylation of the response regulator (RR) ChrA by the kinase HrrS and BACTH assays revealed the formation of heterodimers between HrrS and ChrS. Overall, our results emphasize an important role of the ChrS pseudokinase in high heme tolerance of the evolved C. glutamicum and demonstrate the promiscuity in heme-dependent signaling of the paralogous two-component systems facilitating fast adaptation to changing environmental conditions.
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Diversity in Sensing and Signaling of Bacterial Sensor Histidine Kinases. Biomolecules 2021; 11:biom11101524. [PMID: 34680156 PMCID: PMC8534201 DOI: 10.3390/biom11101524] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/13/2021] [Accepted: 10/13/2021] [Indexed: 11/17/2022] Open
Abstract
Two-component signal transduction systems (TCSs) are widely conserved in bacteria to respond to and adapt to the changing environment. Since TCSs are also involved in controlling the expression of virulence, biofilm formation, quorum sensing, and antimicrobial resistance in pathogens, they serve as candidates for novel drug targets. TCSs consist of a sensor histidine kinase (HK) and its cognate response regulator (RR). Upon perception of a signal, HKs autophosphorylate their conserved histidine residues, followed by phosphotransfer to their partner RRs. The phosphorylated RRs mostly function as transcriptional regulators and control the expression of genes necessary for stress response. HKs sense their specific signals not only in their extracytoplasmic sensor domain but also in their cytoplasmic and transmembrane domains. The signals are sensed either directly or indirectly via cofactors and accessory proteins. Accumulating evidence shows that a single HK can sense and respond to multiple signals in different domains. The underlying molecular mechanisms of how HK activity is controlled by these signals have been extensively studied both biochemically and structurally. In this article, we introduce the wide diversity of signal perception in different domains of HKs, together with their recently clarified structures and molecular mechanisms.
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Gushchin I, Aleksenko VA, Orekhov P, Goncharov IM, Nazarenko VV, Semenov O, Remeeva A, Gordeliy V. Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity. Int J Mol Sci 2021; 22:5933. [PMID: 34072989 PMCID: PMC8199190 DOI: 10.3390/ijms22115933] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/18/2022] Open
Abstract
Under anaerobic conditions, bacteria may utilize nitrates and nitrites as electron acceptors. Sensitivity to nitrous compounds is achieved via several mechanisms, some of which rely on sensor histidine kinases (HKs). The best studied nitrate- and nitrite-sensing HKs (NSHKs) are NarQ and NarX from Escherichia coli. Here, we review the function of NSHKs, analyze their natural diversity, and describe the available structural information. In particular, we show that around 6000 different NSHK sequences forming several distinct clusters may now be found in genomic databases, comprising mostly the genes from Beta- and Gammaproteobacteria as well as from Bacteroidetes and Chloroflexi, including those from anaerobic ammonia oxidation (annamox) communities. We show that the architecture of NSHKs is mostly conserved, although proteins from Bacteroidetes lack the HAMP and GAF-like domains yet sometimes have PAS. We reconcile the variation of NSHK sequences with atomistic models and pinpoint the structural elements important for signal transduction from the sensor domain to the catalytic module over the transmembrane and cytoplasmic regions spanning more than 200 Å.
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Affiliation(s)
- Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Vladimir A. Aleksenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Philipp Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ivan M. Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Vera V. Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
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11
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Bersching K, Jacob S. The Molecular Mechanism of Fludioxonil Action Is Different to Osmotic Stress Sensing. J Fungi (Basel) 2021; 7:jof7050393. [PMID: 34067802 PMCID: PMC8156855 DOI: 10.3390/jof7050393] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/14/2021] [Accepted: 05/14/2021] [Indexed: 11/16/2022] Open
Abstract
The group III two-component hybrid histidine kinase MoHik1p in the filamentous fungus Magnaporthe oryzae is known to be a sensor for external osmotic stress and essential for the fungicidal activity of the phenylpyrrole fludioxonil. The mode of action of fludioxonil has not yet been completely clarified but rather assumed to hyperactivate the high osmolarity glycerol (HOG) signaling pathway. To date, not much is known about the detailed molecular mechanism of how osmotic stress is detected or fungicidal activity is initiated within the HOG pathway. The molecular mechanism of signaling was studied using a mutant strain in which the HisKA signaling domain was modified by an amino acid change of histidine H736 to alanine A736. We found that MoHik1pH736A is as resistant to fludioxonil but not as sensitive to osmotic stress as the null mutant ∆Mohik1. H736 is required for fludioxonil action but is not essential for sensing sorbitol stress. Consequently, this report provides evidence of the difference in the molecular mechanism of fludioxonil action and the perception of osmotic stress. This is an excellent basis to understand the successful phenylpyrrole-fungicides’ mode of action better and will give new ideas to decipher cellular signaling mechanisms.
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12
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Proteolysis and multimerization regulate signaling along the two-component regulatory system AdeRS. iScience 2021; 24:102476. [PMID: 34113820 PMCID: PMC8169943 DOI: 10.1016/j.isci.2021.102476] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 03/15/2021] [Accepted: 04/23/2021] [Indexed: 11/23/2022] Open
Abstract
Bacterial two-component regulatory systems are ubiquitous environment-sensing signal transducers involved in pathogenesis and antibiotic resistance. The Acinetobacter baumannii two-component regulatory system AdeRS is made up of a sensor histidine kinase AdeS and a cognate response regulator AdeR, which together reduce repression of the multidrug-resistant efflux pump AdeABC. Herein we demonstrate that an N-terminal intrinsically disordered tail in AdeR is important for the upregulation of adeABC expression, although it greatly increases the susceptibility of AdeR to proteasome-mediated degradation. We also show that AdeS assembles into a hexameric state that is necessary for its full histidine kinase activity, which appears to occur via cis autophosphorylation. Taken together, this study demonstrates new structural mechanisms through which two-component systems can transduce environmental signals to impact gene expression and enlightens new potential antimicrobial approach by targeting two-component regulatory systems. Crystal structure of AdeR dimer with traceable N-terminal intrinsically disordered region. N-terminal intrinsically disordered region AdeR is involved in proteasome proteolysis. Crystal structure of AdeS catalytic domain demonstrates cis autophosphorylation. AdeS can assemble into hexamer and is crucial for its full kinase activity.
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13
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π-Helix controls activity of oxygen-sensing diguanylate cyclases. Biosci Rep 2021; 40:222070. [PMID: 32039439 PMCID: PMC7033309 DOI: 10.1042/bsr20193602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 11/18/2022] Open
Abstract
The ability of organisms to sense and adapt to oxygen levels in their environment leads to changes in cellular phenotypes, including biofilm formation and virulence. Globin coupled sensors (GCSs) are a family of heme proteins that regulate diverse functions in response to O2 levels, including modulating synthesis of cyclic dimeric guanosine monophosphate (c-di-GMP), a bacterial second messenger that regulates biofilm formation. While GCS proteins have been demonstrated to regulate O2-dependent pathways, the mechanism by which the O2 binding event is transmitted from the globin domain to the cyclase domain is unknown. Using chemical cross-linking and subsequent liquid chromatography-tandem mass spectrometry, diguanylate cyclase (DGC)-containing GCS proteins from Bordetella pertussis (BpeGReg) and Pectobacterium carotovorum (PccGCS) have been demonstrated to form direct interactions between the globin domain and a middle domain π-helix. Additionally, mutation of the π-helix caused major changes in oligomerization and loss of DGC activity. Furthermore, results from assays with isolated globin and DGC domains found that DGC activity is affected by the cognate globin domain, indicating unique interactions between output domain and cognate globin sensor. Based on these studies a compact GCS structure, which depends on the middle domain π-helix for orienting the three domains, is needed for DGC activity and allows for direct sensor domain interactions with both middle and output domains to transmit the O2 binding signal. The insights from the present study improve our understanding of DGC regulation and provide insight into GCS signaling that may lead to the ability to rationally control O2-dependent GCS activity.
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14
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Adam K, Ning J, Reina J, Hunter T. NME/NM23/NDPK and Histidine Phosphorylation. Int J Mol Sci 2020; 21:E5848. [PMID: 32823988 PMCID: PMC7461546 DOI: 10.3390/ijms21165848] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/15/2022] Open
Abstract
The NME (Non-metastatic) family members, also known as NDPKs (nucleoside diphosphate kinases), were originally identified and studied for their nucleoside diphosphate kinase activities. This family of kinases is extremely well conserved through evolution, being found in prokaryotes and eukaryotes, but also diverges enough to create a range of complexity, with homologous members having distinct functions in cells. In addition to nucleoside diphosphate kinase activity, some family members are reported to possess protein-histidine kinase activity, which, because of the lability of phosphohistidine, has been difficult to study due to the experimental challenges and lack of molecular tools. However, over the past few years, new methods to investigate this unstable modification and histidine kinase activity have been reported and scientific interest in this area is growing rapidly. This review presents a global overview of our current knowledge of the NME family and histidine phosphorylation, highlighting the underappreciated protein-histidine kinase activity of NME family members, specifically in human cells. In parallel, information about the structural and functional aspects of the NME family, and the knowns and unknowns of histidine kinase involvement in cell signaling are summarized.
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Affiliation(s)
| | | | | | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; (K.A.); (J.N.); (J.R.)
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15
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Zhang L, Wei Y, Tao Y, Zhao S, Wei X, Yin X, Liu S, Niu Q. Molecular mechanism of the smart attack of pathogenic bacteria on nematodes. Microb Biotechnol 2020; 13:683-705. [PMID: 31730281 PMCID: PMC7111092 DOI: 10.1111/1751-7915.13508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 10/16/2019] [Accepted: 10/20/2019] [Indexed: 11/28/2022] Open
Abstract
Nematode-bacterial associations are far-reaching subjects in view of their impact on ecosystems, economies, agriculture and human health. There is still no conclusion regarding which pathogenic bacteria sense nematodes. Here, we found that the pathogenic bacterium Bacillus nematocida B16 was sensitive to C. elegans and could launch smart attacks to kill the nematodes. Further analysis revealed that the spores of B. nematocida B16 are essential virulence factors. Once gaseous molecules (morpholine) produced from C. elegans were sensed, the sporulation of B16 was greatly accelerated. Then, B16 showed maximum attraction to C. elegans during the spore-forming process but had no attraction until all the spores were formed. The disruption of either the spore formation gene spo0A or the germination gene gerD impaired colonization and attenuated infection in B16. In contrast, complementation with the intact genes restored most of the above-mentioned deficient phenotypes, which indicated that the spo0A gene was a key factor in the smart attack of B16 on C. elegans. Further, transcriptome, molecular simulations and quantitative PCR analysis showed that morpholine from C. elegans could promote sporulation and initiate infection by increasing the transcription of the spo0A gene by decreasing the transcription of the rapA and spo0E genes. The overexpression of rapA or spo0E decreased the induced sporulation effect, and morpholine directly reduced the level of phosphorylation of purified recombinant RapA and Spo0E compared to that of Spo0A. Collectively, these findings further support a 'Trojan horse-like' infection model. The significance of our paper is that we showed that the soil-dwelling bacterium B. nematocida B16 has the ability to actively detect, attract and attack their host C. elegans. These studies are the first report on the behaviours, signalling molecules and mechanism of the smart attack of B16 on nematodes and also reveal new insights into microbe-host interactions.
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Affiliation(s)
- Lin Zhang
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
- State Key Laboratory of Cotton BiologyHenan Key Laboratory of Plant Stress BiologySchool of Life SciencesHenan UniversityKaifengHenan475001China
| | - Yuping Wei
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Ye Tao
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Suya Zhao
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Xuyang Wei
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Xiaoyan Yin
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Suyao Liu
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Qiuhong Niu
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
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16
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Bouillet S, Wu T, Chen S, Stock AM, Gao R. Structural asymmetry does not indicate hemiphosphorylation in the bacterial histidine kinase CpxA. J Biol Chem 2020; 295:8106-8117. [PMID: 32094228 DOI: 10.1074/jbc.ra120.012757] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/19/2020] [Indexed: 11/06/2022] Open
Abstract
Histidine protein kinases (HKs) are prevalent prokaryotic sensor kinases that are central to phosphotransfer in two-component signal transduction systems, regulating phosphorylation of response regulator proteins that determine the output responses. HKs typically exist as dimers and can potentially autophosphorylate at each conserved histidine residue in the individual protomers, leading to diphosphorylation. However, analyses of HK phosphorylation in biochemical assays in vitro suggest negative cooperativity, whereby phosphorylation in one protomer of the dimer inhibits phosphorylation in the second protomer, leading to ∼50% phosphorylation of the available sites in dimers. This negative cooperativity is often correlated with an asymmetric domain arrangement, a common structural characteristic of autophosphorylation states in many HK structures. In this study, we engineered covalent dimers of the cytoplasmic domains of Escherichia coli CpxA, enabling us to quantify individual species: unphosphorylated, monophosphorylated, and diphosphorylated dimers. Together with mathematical modeling, we unambiguously demonstrate no cooperativity in autophosphorylation of CpxA despite its asymmetric structures, indicating that these asymmetric domain arrangements are not linked to negative cooperativity and hemiphosphorylation. Furthermore, the modeling indicated that many parameters, most notably minor amounts of ADP generated during autophosphorylation reactions or present in ATP preparations, can produce ∼50% total phosphorylation that may be mistakenly attributed to negative cooperativity. This study also establishes that the engineered covalent heterodimer provides a robust experimental system for investigating cooperativity in HK autophosphorylation and offers a useful tool for testing how symmetric or asymmetric structural features influence HK functions.
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Affiliation(s)
- Sophie Bouillet
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854
| | - Ti Wu
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854
| | - Shaoxing Chen
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854
| | - Ann M Stock
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854
| | - Rong Gao
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854
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17
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Samanta S, Biswas P, Banerjee A, Bose A, Siddiqui N, Nambi S, Saini DK, Visweswariah SS. A universal stress protein in Mycobacterium smegmatis sequesters the cAMP-regulated lysine acyltransferase and is essential for biofilm formation. J Biol Chem 2020; 295:1500-1516. [PMID: 31882539 PMCID: PMC7008380 DOI: 10.1074/jbc.ra119.011373] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/19/2019] [Indexed: 01/08/2023] Open
Abstract
Universal stress proteins (USPs) are present in many bacteria, and their expression is enhanced under various environmental stresses. We have previously identified a USP in Mycobacterium smegmatis that is a product of the msmeg_4207 gene and is a substrate for a cAMP-regulated protein lysine acyltransferase (KATms; MSMEG_5458). Here, we explored the role of this USP (USP4207) in M. smegmatis and found that its gene is present in an operon that also contains genes predicted to encode a putative tripartite tricarboxylate transporter (TTT). Transcription of the TTT-usp4207 operon was induced in the presence of citrate and tartrate, perhaps by the activity of a divergent histidine kinase-response regulator gene pair. A usp4207-deleted strain had rough colony morphology and reduced biofilm formation compared with the WT strain; however, both normal colony morphology and biofilm formation were restored in a Δusp4207Δkatms strain. We identified several proteins whose acetylation was lost in the Δkatms strain, and whose transcript levels increased in M. smegmatis biofilms along with that of USP4207, suggesting that USP4207 insulates KATms from its other substrates in the cell. We propose that USP4207 sequesters KATms from diverse substrates whose activities are down-regulated by acylation but are required for biofilm formation, thus providing a defined role for this USP in mycobacterial physiology and stress responses.
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Affiliation(s)
- Sintu Samanta
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Priyanka Biswas
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Arka Banerjee
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Avipsa Bose
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Nida Siddiqui
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Subhalaxmi Nambi
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Deepak Kumar Saini
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Sandhya S Visweswariah
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India.
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18
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Skalova T, Lengalova A, Dohnalek J, Harlos K, Mihalcin P, Kolenko P, Stranava M, Blaha J, Shimizu T, Martínková M. Disruption of the dimerization interface of the sensing domain in the dimeric heme-based oxygen sensor AfGcHK abolishes bacterial signal transduction. J Biol Chem 2020; 295:1587-1597. [PMID: 31914416 PMCID: PMC7008379 DOI: 10.1074/jbc.ra119.011574] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/30/2019] [Indexed: 12/17/2022] Open
Abstract
The heme-based oxygen sensor protein AfGcHK is a globin-coupled histidine kinase in the soil bacterium Anaeromyxobacter sp. Fw109-5. Its C-terminal functional domain exhibits autophosphorylation activity induced by oxygen binding to the heme-Fe(II) complex located in the oxygen-sensing N-terminal globin domain. A detailed understanding of the signal transduction mechanisms in heme-containing sensor proteins remains elusive. Here, we investigated the role of the globin domain's dimerization interface in signal transduction in AfGcHK. We present a crystal structure of a monomeric imidazole-bound AfGcHK globin domain at 1.8 Å resolution, revealing that the helices of the WT globin dimer are under tension and suggesting that Tyr-15 plays a role in both this tension and the globin domain's dimerization. Biophysical experiments revealed that whereas the isolated WT globin domain is dimeric in solution, the Y15A and Y15G variants in which Tyr-15 is replaced with Ala or Gly, respectively, are monomeric. Additionally, we found that although the dimerization of the full-length protein is preserved via the kinase domain dimerization interface in all variants, full-length AfGcHK variants bearing the Y15A or Y15G substitutions lack enzymatic activity. The combined structural and biophysical results presented here indicate that Tyr-15 plays a key role in the dimerization of the globin domain of AfGcHK and that globin domain dimerization is essential for internal signal transduction and autophosphorylation in this protein. These findings provide critical insights into the signal transduction mechanism of the histidine kinase AfGcHK from Anaeromyxobacter.
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Affiliation(s)
- Tereza Skalova
- Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Biocev, Vestec, 252 50 Czech Republic
| | - Alzbeta Lengalova
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, 128 43 Czech Republic
| | - Jan Dohnalek
- Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Biocev, Vestec, 252 50 Czech Republic
| | - Karl Harlos
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, United Kingdom
| | - Peter Mihalcin
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, 128 43 Czech Republic
| | - Petr Kolenko
- Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Biocev, Vestec, 252 50 Czech Republic; FNSPE, Czech Technical University in Prague, Brehova 7, Prague 1, 115 19 Czech Republic
| | - Martin Stranava
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, 128 43 Czech Republic
| | - Jan Blaha
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, 128 43 Czech Republic
| | - Toru Shimizu
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, 128 43 Czech Republic
| | - Markéta Martínková
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, 128 43 Czech Republic.
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19
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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: 17] [Impact Index Per Article: 4.3] [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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20
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Götze S, Stallforth P. Structure, properties, and biological functions of nonribosomal lipopeptides from pseudomonads. Nat Prod Rep 2020; 37:29-54. [DOI: 10.1039/c9np00022d] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Bacteria of the genusPseudomonasdisplay a fascinating metabolic diversity. In this review, we focus our attention on the natural product class of nonribosomal lipopeptides, which help pseudomonads to colonize a wide range of ecological niches.
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Affiliation(s)
- Sebastian Götze
- Faculty 7: Natural and Environmental Sciences
- Institute for Environmental Sciences
- University Koblenz Landau
- 76829 Landau
- Germany
| | - Pierre Stallforth
- Junior Research Group Chemistry of Microbial Communication
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)
- 07745 Jena
- Germany
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21
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Guła G, Dorotkiewicz-Jach A, Korzekwa K, Valvano MA, Drulis-Kawa Z. Complex Signaling Networks Controlling Dynamic Molecular Changes in Pseudomonas aeruginosa Biofilm. Curr Med Chem 2019; 26:1979-1993. [PMID: 30207213 DOI: 10.2174/0929867325666180912110151] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/11/2018] [Accepted: 08/31/2018] [Indexed: 02/06/2023]
Abstract
The environment exerts strong influence on microbes. Adaptation of microbes to changing conditions is a dynamic process regulated by complex networks. Pseudomonas aeruginosa is a life-threating, versatile opportunistic and multi drug resistant pathogen that provides a model to investigate adaptation mechanisms to environmental changes. The ability of P. aeruginosa to form biofilms and to modify virulence in response to environmental changes is coordinated by various mechanisms including two-component systems (TCS), and secondary messengers involved in quorum sensing (QS) and c-di-GMP networks (diguanylate cyclase systems, DGC). In this review, we focus on the role of c-di-GMP during biofilm formation. We describe TCS and QS signal cascades regulated by c-di-GMP in response to changes in the external environment. We present a complex signaling network dynamically changing during the transition of P. aeruginosa from the free-living to sessile mode of growth.
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Affiliation(s)
- Grzegorz Guła
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
| | - Agata Dorotkiewicz-Jach
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
| | - Kamila Korzekwa
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
| | - Miguel A Valvano
- Wellcome- Wolfson Institute for Experimental Medicine, Queen's University Belfast, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
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22
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Reyes Ruiz LM, Fiebig A, Crosson S. Regulation of bacterial surface attachment by a network of sensory transduction proteins. PLoS Genet 2019; 15:e1008022. [PMID: 31075103 PMCID: PMC6530869 DOI: 10.1371/journal.pgen.1008022] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/22/2019] [Accepted: 04/26/2019] [Indexed: 11/25/2022] Open
Abstract
Bacteria are often attached to surfaces in natural ecosystems. A surface-associated lifestyle can have advantages, but shifts in the physiochemical state of the environment may result in conditions in which attachment has a negative fitness impact. Therefore, bacteria employ numerous mechanisms to control the transition from an unattached to a sessile state. The Caulobacter crescentus protein HfiA is a potent developmental inhibitor of the secreted polysaccharide adhesin known as the holdfast, which enables permanent attachment to surfaces. Multiple environmental cues influence expression of hfiA, but mechanisms of hfiA regulation remain largely undefined. Through a forward genetic selection, we have discovered a multi-gene network encoding a suite of two-component system (TCS) proteins and transcription factors that coordinately control hfiA transcription, holdfast development and surface adhesion. The hybrid HWE-family histidine kinase, SkaH, is central among these regulators and forms heteromeric complexes with the kinases, LovK and SpdS. The response regulator SpdR indirectly inhibits hfiA expression by activating two XRE-family transcription factors that directly bind the hfiA promoter to repress its transcription. This study provides evidence for a model in which a consortium of environmental sensors and transcriptional regulators integrate environmental cues at the hfiA promoter to control the attachment decision. Living on a surface within a community of cells confers a number of advantages to a bacterium. However, the transition from a free-living, planktonic state to a surface-attached lifestyle should be tightly regulated to ensure that cells avoid adhering to toxic or resource-limited niches. Many bacteria build adhesive structures on the surface of their cell envelopes that enable attachment. We sought to discover genes that control development of the Caulobacter crescentus surface adhesin known as the holdfast. Our studies uncovered a network of signal transduction proteins that coordinately control the biosynthesis of the holdfast by regulating transcription of the holdfast inhibitor, hfiA. We conclude that C. crescentus uses a multi-component regulatory system to sense and integrate environmental information to determine whether to attach to a surface, or to remain in an unattached state.
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Affiliation(s)
- Leila M Reyes Ruiz
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Aretha Fiebig
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois United States of America
| | - Sean Crosson
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, Illinois, United States of America.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois United States of America.,Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
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23
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Mancl JM, Ray WK, Helm RF, Schubot FD. Helix Cracking Regulates the Critical Interaction between RetS and GacS in Pseudomonas aeruginosa. Structure 2019; 27:785-793.e5. [PMID: 30879888 DOI: 10.1016/j.str.2019.02.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/07/2019] [Accepted: 02/15/2019] [Indexed: 12/13/2022]
Abstract
Recent paradigm shifting discoveries have demonstrated that bacterial signaling kinases engage in unexpected regulatory crosstalk, yet the underlying molecular mechanisms remain largely uncharacterized. The Pseudomonas aeruginosa RetS/GacS system constitutes an ideal model for studying these mechanisms. The in-depth analysis of the kinase region of RetS and RetS/GacS interactions presented here refutes a longstanding model, which posited the formation of a catalytically inactive RetS/GacS heterodimer. Crystallographic studies uncovered structurally dynamic features within the RetS kinase region, suggesting that RetS uses the reversible unfolding of a helix, or helix cracking, to control interactions with GacS. The pivotal importance of this helical region for regulating GacS and, by extension, Pseudomonas aeruginosa virulence, was corroborated via in vivo assays. The implications of this work extend beyond the RetS/GacS system because the helix cracking occurs right next to a highly conserved catalytic residue histidine-424, suggesting this model could represent an emergent archetype for histidine kinase regulation.
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Affiliation(s)
- Jordan M Mancl
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - William K Ray
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Rich F Helm
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Florian D Schubot
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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24
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Abstract
Spatial control of intracellular signaling relies on signaling proteins sensing their subcellular environment. In many cases, a large number of upstream signals are funneled to a master regulator of cellular behavior, but it remains unclear how individual proteins can rapidly integrate a complex array of signals within the appropriate spatial niche within the cell. As a model for how subcellular spatial information can control signaling activity, we have reconstituted the cell pole-specific control of the master regulator kinase/phosphatase CckA from the asymmetrically dividing bacterium Caulobacter crescentus CckA is active as a kinase only when it accumulates within a microdomain at the new cell pole, where it colocalizes with the pseudokinase DivL. Both proteins contain multiple PAS domains, a multifunctional class of sensory domains present across the kingdoms of life. Here, we show that CckA uses its PAS domains to integrate information from DivL and its own oligomerization state to control the balance of its kinase and phosphatase activities. We reconstituted the DivL-CckA complex on liposomes in vitro and found that DivL directly controls the CckA kinase/phosphatase switch, and that stimulation of either CckA catalytic activity depends on the second of its two PAS domains. We further show that CckA oligomerizes through a multidomain interaction that is critical for stimulation of kinase activity by DivL, while DivL stimulation of CckA phosphatase activity is independent of CckA homooligomerization. Our results broadly demonstrate how signaling factors can leverage information from their subcellular niche to drive spatiotemporal control of cell signaling.
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25
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Francis VI, Waters EM, Finton-James SE, Gori A, Kadioglu A, Brown AR, Porter SL. Multiple communication mechanisms between sensor kinases are crucial for virulence in Pseudomonas aeruginosa. Nat Commun 2018; 9:2219. [PMID: 29880803 PMCID: PMC5992135 DOI: 10.1038/s41467-018-04640-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 05/14/2018] [Indexed: 12/16/2022] Open
Abstract
Bacteria and many non-metazoan Eukaryotes respond to stresses and threats using two-component systems (TCSs) comprising sensor kinases (SKs) and response regulators (RRs). Multikinase networks, where multiple SKs work together, detect and integrate different signals to control important lifestyle decisions such as sporulation and virulence. Here, we study interactions between two SKs from Pseudomonas aeruginosa, GacS and RetS, which control the switch between acute and chronic virulence. We demonstrate three mechanisms by which RetS attenuates GacS signalling: RetS takes phosphoryl groups from GacS-P; RetS has transmitter phosphatase activity against the receiver domain of GacS-P; and RetS inhibits GacS autophosphorylation. These mechanisms play important roles in vivo and during infection, and exemplify an unprecedented degree of signal processing by SKs that may be exploited in other multikinase networks.
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Affiliation(s)
- Vanessa I Francis
- Biosciences, Geoffrey Pope Building, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Elaine M Waters
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Sutharsan E Finton-James
- Biosciences, Geoffrey Pope Building, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Andrea Gori
- Biosciences, Geoffrey Pope Building, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Alan R Brown
- Biosciences, Geoffrey Pope Building, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Steven L Porter
- Biosciences, Geoffrey Pope Building, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK.
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26
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Francis VI, Stevenson EC, Porter SL. Two-component systems required for virulence in Pseudomonas aeruginosa. FEMS Microbiol Lett 2018; 364:3828290. [PMID: 28510688 PMCID: PMC5812489 DOI: 10.1093/femsle/fnx104] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 05/15/2017] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa is a versatile opportunistic pathogen capable of infecting a broad range of hosts, in addition to thriving in a broad range of environmental conditions outside of hosts. With this versatility comes the need to tightly regulate its genome to optimise its gene expression and behaviour to the prevailing conditions. Two-component systems (TCSs) comprising sensor kinases and response regulators play a major role in this regulation. This minireview discusses the growing number of TCSs that have been implicated in the virulence of P. aeruginosa, with a special focus on the emerging theme of multikinase networks, which are networks comprising multiple sensor kinases working together, sensing and integrating multiple signals to decide upon the best response. The networks covered in depth regulate processes such as the switch between acute and chronic virulence (GacS network), the Cup fimbriae (Roc network and Rcs/Pvr network), the aminoarabinose modification of lipopolysaccharide (a network involving the PhoQP and PmrBA TCSs), twitching motility and virulence (a network formed from the Chp chemosensory pathway and the FimS/AlgR TCS), and biofilm formation (Wsp chemosensory pathway). In addition, we highlight the important interfaces between these systems and secondary messenger signals such as cAMP and c-di-GMP.
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Affiliation(s)
- Vanessa I Francis
- Biosciences, Geoffrey Pope Building, College of Life and Environmental Sciences, University of Exeter, Exeter EX 4QD, UK
| | - Emma C Stevenson
- Biosciences, Geoffrey Pope Building, College of Life and Environmental Sciences, University of Exeter, Exeter EX 4QD, UK
| | - Steven L Porter
- Biosciences, Geoffrey Pope Building, College of Life and Environmental Sciences, University of Exeter, Exeter EX 4QD, UK
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27
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Stranava M, Man P, Skálová T, Kolenko P, Blaha J, Fojtikova V, Martínek V, Dohnálek J, Lengalova A, Rosůlek M, Shimizu T, Martínková M. Coordination and redox state-dependent structural changes of the heme-based oxygen sensor AfGcHK associated with intraprotein signal transduction. J Biol Chem 2017; 292:20921-20935. [PMID: 29092908 DOI: 10.1074/jbc.m117.817023] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/18/2017] [Indexed: 11/06/2022] Open
Abstract
The heme-based oxygen sensor histidine kinase AfGcHK is part of a two-component signal transduction system in bacteria. O2 binding to the Fe(II) heme complex of its N-terminal globin domain strongly stimulates autophosphorylation at His183 in its C-terminal kinase domain. The 6-coordinate heme Fe(III)-OH- and -CN- complexes of AfGcHK are also active, but the 5-coordinate heme Fe(II) complex and the heme-free apo-form are inactive. Here, we determined the crystal structures of the isolated dimeric globin domains of the active Fe(III)-CN- and inactive 5-coordinate Fe(II) forms, revealing striking structural differences on the heme-proximal side of the globin domain. Using hydrogen/deuterium exchange coupled with mass spectrometry to characterize the conformations of the active and inactive forms of full-length AfGcHK in solution, we investigated the intramolecular signal transduction mechanisms. Major differences between the active and inactive forms were observed on the heme-proximal side (helix H5), at the dimerization interface (helices H6 and H7 and loop L7) of the globin domain and in the ATP-binding site (helices H9 and H11) of the kinase domain. Moreover, separation of the sensor and kinase domains, which deactivates catalysis, increased the solvent exposure of the globin domain-dimerization interface (helix H6) as well as the flexibility and solvent exposure of helix H11. Together, these results suggest that structural changes at the heme-proximal side, the globin domain-dimerization interface, and the ATP-binding site are important in the signal transduction mechanism of AfGcHK. We conclude that AfGcHK functions as an ensemble of molecules sampling at least two conformational states.
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Affiliation(s)
- Martin Stranava
- From the Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, 128 43 Czech Republic
| | - Petr Man
- From the Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, 128 43 Czech Republic.,the Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Biocev, 252 50 Vestec, Czech Republic
| | - Tereza Skálová
- the Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Biocev, 252 50 Vestec, Czech Republic, and
| | - Petr Kolenko
- the Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Biocev, 252 50 Vestec, Czech Republic, and.,the Department of Solid State Engineering, Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Brehova 7, 115 19 Praha 1, Czech Republic
| | - Jan Blaha
- From the Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, 128 43 Czech Republic
| | - Veronika Fojtikova
- From the Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, 128 43 Czech Republic
| | - Václav Martínek
- From the Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, 128 43 Czech Republic
| | - Jan Dohnálek
- the Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Biocev, 252 50 Vestec, Czech Republic, and
| | - Alzbeta Lengalova
- From the Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, 128 43 Czech Republic
| | - Michal Rosůlek
- From the Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, 128 43 Czech Republic.,the Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Biocev, 252 50 Vestec, Czech Republic
| | - Toru Shimizu
- From the Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, 128 43 Czech Republic
| | - Markéta Martínková
- From the Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, 128 43 Czech Republic,
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