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Dey S, Shahrear S, Afroj Zinnia M, Tajwar A, Islam ABMMK. Functional Annotation of Hypothetical Proteins From the Enterobacter cloacae B13 Strain and Its Association With Pathogenicity. Bioinform Biol Insights 2022; 16:11779322221115535. [PMID: 35958299 PMCID: PMC9358594 DOI: 10.1177/11779322221115535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/11/2022] [Indexed: 11/25/2022] Open
Abstract
Enterobacter cloacae B13 strain is a rod-shaped gram-negative bacterium that belongs to the Enterobacteriaceae family. It can cause respiratory and urinary tract infections, and is responsible for several outbreaks in hospitals. E. cloacae has become an important pathogen and an emerging global threat because of its opportunistic and multidrug resistant ability. However, little knowledge is present about a large portion of its proteins and functions. Therefore, functional annotation of the hypothetical proteins (HPs) can provide an improved understanding of this organism and its virulence activity. The workflow in the study included several bioinformatic tools which were utilized to characterize functions, family and domains, subcellular localization, physiochemical properties, and protein-protein interactions. The E. cloacae B13 strain has overall 604 HPs, among which 78 were functionally annotated with high confidence. Several proteins were identified as enzymes, regulatory, binding, and transmembrane proteins with essential functions. Furthermore, 23 HPs were predicted to be virulent factors. These virulent proteins are linked to pathogenesis with their contribution to biofilm formation, quorum sensing, 2-component signal transduction or secretion. Better knowledge about the HPs’ characteristics and functions will provide a greater overview of the proteome. Moreover, it will help against E. cloacae in neonatal intensive care unit (NICU) outbreaks and nosocomial infections.
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Affiliation(s)
- Supantha Dey
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Sazzad Shahrear
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | | | - Ahnaf Tajwar
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
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Tiwari M, Mishra AK, Chakrabarty D. Agrobacterium-mediated gene transfer: recent advancements and layered immunity in plants. PLANTA 2022; 256:37. [PMID: 35819629 PMCID: PMC9274631 DOI: 10.1007/s00425-022-03951-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/19/2022] [Indexed: 05/15/2023]
Abstract
Plant responds to Agrobacterium via three-layered immunity that determines its susceptibility or resistance to Agrobacterium infection. Agrobacterium tumefaciens is a soil-borne Gram-negative bacterium that causes crown gall disease in plants. The remarkable feat of interkingdom gene transfer has been extensively utilised in plant biotechnology to transform plant as well as non-host systems. In the past two decades, the molecular mode of the pathogenesis of A. tumefaciens has been extensively studied. Agrobacterium has also been utilised as a premier model to understand the defence response of plants during plant-Agrobacterium interaction. Nonetheless, the threat of Agrobacterium-mediated crown gall disease persists and is associated with a huge loss of plant vigour in agriculture. Understanding the molecular dialogues between these two interkingdom species might provide a cure for crown gall disease. Plants respond to A. tumefaciens by mounting a three-layered immune response, which is manipulated by Agrobacterium via its virulence effector proteins. Comparative studies on plant defence proteins versus the counter-defence of Agrobacterium have shed light on plant susceptibility and tolerance. It is possible to manipulate a plant's immune system to overcome the crown gall disease and increase its competence via A. tumefaciens-mediated transformation. This review summarises the recent advances in the molecular mode of Agrobacterium pathogenesis as well as the three-layered immune response of plants against Agrobacterium infection.
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Affiliation(s)
- Madhu Tiwari
- Biotechnology and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India
| | - Arun Kumar Mishra
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India
| | - Debasis Chakrabarty
- Biotechnology and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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3
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Swackhammer A, Provencher EAP, Donkor AK, Garofalo J, Dowling S, Garchitorena K, Phyo A, Ramírez Veliz N, Karen M, Kwon A, Diep R, Norris M, Safo MK, Pierce BD. Mechanistic Analysis of the VirA Sensor Kinase in Agrobacterium tumefaciens Using Structural Models. Front Microbiol 2022; 13:898785. [PMID: 35651496 PMCID: PMC9149312 DOI: 10.3389/fmicb.2022.898785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Agrobacterium tumefaciens pathogenesis of plants is initiated with signal reception and culminates with transforming the genomic DNA of its host. The histidine sensor kinase VirA receives and reacts to discrete signaling molecules for the full induction of the genes necessary for this process. Though many of the components of this process have been identified, the precise mechanism of how VirA coordinates the response to host signals, namely phenols and sugars, is unknown. Recent advances of molecular modeling have allowed us to test structure/function predictions and contextualize previous experiments with VirA. In particular, the deep mind software AlphaFold has generated a structural model for the entire protein, allowing us to construct a model that addresses the mechanism of VirA signal reception. Here, we deepen our analysis of the region of VirA that is critical for phenol reception, model and probe potential phenol-binding sites of VirA, and refine its mechanism to strengthen our understanding of A. tumefaciens signal perception.
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Affiliation(s)
| | - Edward A. P. Provencher
- Department of Biology, University of Richmond, Richmond, VA, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, PA, United States
| | - Akua K. Donkor
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, United States
| | - Jessica Garofalo
- Department of Biology, University of Richmond, Richmond, VA, United States
| | - Sinead Dowling
- Department of Biology, University of Richmond, Richmond, VA, United States
| | | | - Ahkar Phyo
- Department of Biology, University of Richmond, Richmond, VA, United States
| | | | - Matthew Karen
- Department of Biology, University of Richmond, Richmond, VA, United States
| | - Annie Kwon
- Department of Biology, University of Richmond, Richmond, VA, United States
| | - Rich Diep
- Department of Biology, University of Richmond, Richmond, VA, United States
| | - Michael Norris
- Department of Chemistry, University of Richmond, Richmond, VA, United States
| | - Martin K. Safo
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, United States
| | - B. Daniel Pierce
- Department of Biology, University of Richmond, Richmond, VA, United States
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Lazar JT, Tabor JJ. Bacterial two-component systems as sensors for synthetic biology applications. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 28:100398. [PMID: 34917859 PMCID: PMC8670732 DOI: 10.1016/j.coisb.2021.100398] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Two-component systems (TCSs) are a ubiquitous family of signal transduction pathways that enable bacteria to sense and respond to diverse physical, chemical, and biological stimuli outside and inside the cell. Synthetic biologists have begun to repurpose TCSs for applications in optogenetics, materials science, gut microbiome engineering, and soil nutrient biosensing, among others. New engineering methods including genetic refactoring, DNA-binding domain swapping, detection threshold tuning, and phosphorylation cross-talk insulation are being used to increase the reliability of TCS sensor performance and tailor TCS signaling properties to the requirements of specific applications. There is now potential to combine these methods with large-scale gene synthesis and laboratory screening to discover the inputs sensed by many uncharacterized TCSs and develop a large new family of genetically-encoded sensors that respond to an unrivaled breadth of stimuli.
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Affiliation(s)
- John T Lazar
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Jeffrey J Tabor
- Department of Bioengineering, Rice University, Houston, TX, USA
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
- Department of Biosciences, Rice University, Houston, TX, USA
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De Saeger J, Park J, Chung HS, Hernalsteens JP, Van Lijsebettens M, Inzé D, Van Montagu M, Depuydt S. Agrobacterium strains and strain improvement: Present and outlook. Biotechnol Adv 2020; 53:107677. [PMID: 33290822 DOI: 10.1016/j.biotechadv.2020.107677] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 11/03/2020] [Accepted: 11/28/2020] [Indexed: 12/12/2022]
Abstract
Almost 40 years ago the first transgenic plant was generated through Agrobacterium tumefaciens-mediated transformation, which, until now, remains the method of choice for gene delivery into plants. Ever since, optimized Agrobacterium strains have been developed with additional (genetic) modifications that were mostly aimed at enhancing the transformation efficiency, although an optimized strain also exists that reduces unwanted plasmid recombination. As a result, a collection of very useful strains has been created to transform a wide variety of plant species, but has also led to a confusing Agrobacterium strain nomenclature. The latter is often misleading for choosing the best-suited strain for one's transformation purposes. To overcome this issue, we provide a complete overview of the strain classification. We also indicate different strain modifications and their purposes, as well as the obtained results with regard to the transformation process sensu largo. Furthermore, we propose additional improvements of the Agrobacterium-mediated transformation process and consider several worthwhile modifications, for instance, by circumventing a defense response in planta. In this regard, we will discuss pattern-triggered immunity, pathogen-associated molecular pattern detection, hormone homeostasis and signaling, and reactive oxygen species in relationship to Agrobacterium transformation. We will also explore alterations that increase agrobacterial transformation efficiency, reduce plasmid recombination, and improve biocontainment. Finally, we recommend the use of a modular system to best utilize the available knowledge for successful plant transformation.
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Affiliation(s)
- Jonas De Saeger
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon 406-840, South Korea; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Jihae Park
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon 406-840, South Korea; Department of Marine Sciences, Incheon National University, Incheon 406-840, South Korea
| | - Hoo Sun Chung
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | | | - Mieke Van Lijsebettens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Marc Van Montagu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Stephen Depuydt
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon 406-840, South Korea; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium.
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Song S, Yan R, Wang C, Wang J, Sun H. Improvement of a Genetic Transformation System and Preliminary Study on the Function of LpABCB21 and LpPILS7 Based on Somatic Embryogenesis in Lilium pumilum DC. Fisch. Int J Mol Sci 2020; 21:E6784. [PMID: 32947885 PMCID: PMC7554901 DOI: 10.3390/ijms21186784] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/07/2020] [Accepted: 09/14/2020] [Indexed: 11/16/2022] Open
Abstract
Auxin transport mediates the asymmetric distribution of auxin that determines the fate of cell development. Agrobacterium-mediated genetic transformation is an important technical means to study gene function. Our previous study showed that the expression levels of LpABCB21 and LpPILS7 are significantly up-regulated in the somatic embryogenesis (SE) of Lilium pumilum DC. Fisch. (L. pumilum), but the functions of both genes remain unclear. Here, the genetic transformation technology previously developed by our team based on the L. pumilum system was improved, and the genetic transformation efficiency increased by 5.7-13.0%. Use of overexpression and CRISPR/Cas9 technology produced three overexpression and seven mutant lines of LpABCB21, and seven overexpression and six mutant lines of LpPILS7. Analysis of the differences in somatic embryo induction of transgenic lines confirmed that LpABCB21 regulates the early formation of the somatic embryo; however, excessive expression level of LpABCB21 inhibits somatic embryo induction efficiency. LpPILS7 mainly regulates somatic embryo induction efficiency. This study provides a more efficient method of genetic transformation of L. pumilum. LpABCB21 and LpPILS7 are confirmed to have important regulatory roles in L. pumilum SE thus laying the foundation for subsequent studies of the molecular mechanism of Lilium SE.
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Affiliation(s)
- Shengli Song
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (S.S.); (R.Y.); (C.W.); (J.W.)
| | - Rui Yan
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (S.S.); (R.Y.); (C.W.); (J.W.)
| | - Chunxia Wang
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (S.S.); (R.Y.); (C.W.); (J.W.)
| | - Jinxia Wang
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (S.S.); (R.Y.); (C.W.); (J.W.)
| | - Hongmei Sun
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (S.S.); (R.Y.); (C.W.); (J.W.)
- National and Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology, Shenyang 110866, China
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7
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Kowallis KA, Silfani EM, Kasumu AP, Rong G, So V, Childers WS. Synthetic Control of Signal Flow Within a Bacterial Multi-Kinase Network. ACS Synth Biol 2020; 9:1705-1713. [PMID: 32559383 DOI: 10.1021/acssynbio.0c00043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The signal processing capabilities of bacterial signaling networks offer immense potential for advanced phospho-signaling systems for synthetic biology. Emerging models suggest that complex development may require interconnections between what were once thought to be isolated signaling arrays. For example, Caulobacter crescentus achieves the feat of asymmetric division by utilizing a novel pseudokinase DivL, which senses the output of one signaling pathway to modulate a second pathway. It has been proposed that DivL reverses signal flow by exploiting conserved kinase conformational changes and protein-protein interactions. We engineered a series of DivL-based modulators to synthetically stimulate reverse signaling of the network in vivo. Stimulation of conformational changes through the DivL signal transmission helix resulted in changes to hallmark features of the network: C. crescentus motility and DivL accumulation at the cell poles. Additionally, mutations to a conserved PAS sensor transmission motif disrupted reverse signaling flow in vivo. We propose that synthetic stimulation and sensor disruption provide strategies to define signaling circuit organization principles for the rational design and validation of synthetic pathways.
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Affiliation(s)
- Kimberly A. Kowallis
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Elayna M. Silfani
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Amanda P. Kasumu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Grace Rong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Victor So
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - W. Seth Childers
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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8
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Liu S, Lin YH, Murphy A, Anderson J, Walker N, Lynn DG, Binns AN, Pierce BD. Mapping Reaction-Diffusion Networks at the Plant Wound Site With Pathogens. FRONTIERS IN PLANT SCIENCE 2020; 11:1074. [PMID: 32765558 PMCID: PMC7379035 DOI: 10.3389/fpls.2020.01074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/30/2020] [Indexed: 06/11/2023]
Abstract
The rich collection of microbes colonizing the plant root making up the rhizosphere function as a multigenomic organ for nutrient distribution. The extent to which its dynamic mutualistic cellular order depends on morphogenic signaling, while likely, remains unknown. We have shown that reaction-diffusion chemical networks constructed with model plant and bacterial metabolites can mimic processes ranging from oxidative burst kinetics to traveling waves and extracellular stationary state reaction-diffusion networks for spatiotemporal ordering of the rhizosphere. Plant parasites and pathogens can be limited by host attachment require dynamic informational networks and continue to provide insight into what controls the rhizosphere. Here we take advantage of Agrobacterium tumefaciens, a plant pathogen with a gated receptor that requires simultaneous perception of two plant metabolites. Genetic manipulations have created receptors allowing each metabolite concentration to be correlated with pathogen behavior. The development of the florescent strains used here provide initial maps of the reaction-diffusion dynamics existing in the rhizosphere, revealing significant differences in the signaling landscape of host and non-host plants before and after wounding, specifically highlighting networks that may inform rhizosphere organization.
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Affiliation(s)
- Stephanie Liu
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, United States
| | - Yi-Han Lin
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, United States
- Infectious Diseases and Genomic Medicine Group, J Craig Venter Institute, Rockville, MD, United States
| | - Aidan Murphy
- Department of Biology, University of Richmond, Richmond, VA, United States
| | - Josh Anderson
- Department of Biology, University of Richmond, Richmond, VA, United States
| | - Nicole Walker
- Department of Biology, University of Richmond, Richmond, VA, United States
| | - David G. Lynn
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, United States
| | - Andrew N. Binns
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
| | - B. Daniel Pierce
- Department of Biology, University of Richmond, Richmond, VA, United States
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9
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Duvall SW, Childers WS. Design of a Histidine Kinase FRET Sensor to Detect Complex Signal Integration within Living Bacteria. ACS Sens 2020; 5:1589-1596. [PMID: 32495620 DOI: 10.1021/acssensors.0c00008] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Histidine kinases (HK) switch between conformational states that promote kinase and phosphatase activities to regulate diverse cellular processes. Past studies have shown that these functional states can display heterogeneity between cells in microbial communities and can vary at the subcellular level. Methods to track and correlate the kinase conformational state with the phenotypic response of living bacteria cells will offer new opportunities to interrogate bacterial signaling mechanisms. As a proof of principle, we incorporated both mClover3 (donor) and mRuby3 (acceptor) fluorescent proteins into the Caulobacter crescentus cell-cycle HK CckA as an in vivo fluorescence resonance energy transfer (FRET) sensor to detect these structural changes. Our engineered FRET sensor was responsive to CckA-specific input signals and detected subcellular changes in CckA signal integration that occurs as cells develop. We demonstrated the potential of using the CckA FRET sensor as an in vivo screening tool for HK inhibitors. In summary, we have developed a new HK FRET sensor design strategy that can be adopted to monitor in vivo changes for interrogation of a broad range of signaling mechanisms in living bacteria.
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Affiliation(s)
- Samuel W. Duvall
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - W. Seth Childers
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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10
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Binns AN, Zhao J. The MexE/MexF/AmeC Efflux Pump of Agrobacterium tumefaciens and Its Role in Ti Plasmid Virulence Gene Expression. J Bacteriol 2020; 202:e00609-19. [PMID: 32015146 PMCID: PMC7099130 DOI: 10.1128/jb.00609-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/25/2020] [Indexed: 12/21/2022] Open
Abstract
Expression of the tumor-inducing (Ti) plasmid virulence genes of Agrobacterium tumefaciens is required for the transfer of DNA from the bacterium into plant cells, ultimately resulting in the initiation of plant tumors. The vir genes are induced as a result of exposure to certain phenol derivatives, monosaccharides, and low pH in the extracellular milieu. The soil, as well as wound sites on a plant-the usual site of the virulence activity of this bacterium-can contain these signals, but vir gene expression in the soil would be a wasteful utilization of energy. This suggests that mechanisms may exist to ensure that vir gene expression occurs only at the higher concentrations of inducers typically found at a plant wound site. In a search for transposon-mediated mutations that affect sensitivity for the virulence gene-inducing activity of the phenol, 3,5-dimethoxy-4-hydroxyacetophenone (acetosyringone [AS]), an RND-type efflux pump homologous to the MexE/MexF/OprN pump of Pseudomonas aeruginosa was identified. Phenotypes of mutants carrying an insertion or deletion of pump components included hypersensitivity to the vir-inducing effects of AS, hypervirulence in the tobacco leaf explant virulence assay, and hypersensitivity to the toxic effects of chloramphenicol. Furthermore, the methoxy substituents on the phenol ring of AS appear to be critical for recognition as a pump substrate. These results support the hypothesis that the regulation of virulence gene expression is integrated with cellular activities that elevate the level of plant-derived inducers required for induction so that this occurs preferentially, if not exclusively, in a plant environment.IMPORTANCE Expression of genes controlling the virulence activities of a bacterial pathogen is expected to occur preferentially at host sites vulnerable to that pathogen. Host-derived molecules that induce such activities in the plant pathogen Agrobacterium tumefaciens are found in the soil, as well as in the plant. Here, we tested the hypothesis that mechanisms exist to suppress the sensitivity of Agrobacterium species to a virulence gene-inducing molecule by selecting for mutant bacteria that are hypersensitive to its inducing activity. The mutant genes identified encode an efflux pump whose proposed activity increases the concentration of the inducer necessary for vir gene expression; this pump is also involved in antibiotic resistance, demonstrating a relationship between cellular defense activities and the control of virulence in Agrobacterium.
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Affiliation(s)
- Andrew N Binns
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jinlei Zhao
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Kowallis KA, Duvall SW, Zhao W, Childers WS. Manipulation of Bacterial Signaling Using Engineered Histidine Kinases. Methods Mol Biol 2020; 2077:141-163. [PMID: 31707657 DOI: 10.1007/978-1-4939-9884-5_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Two-component systems allow bacteria to respond to changes in environmental or cytosolic conditions through autophosphorylation of a histidine kinase (HK) and subsequent transfer of the phosphate group to its downstream cognate response regulator (RR). The RR then elicits a cellular response, commonly through regulation of transcription. Engineering two-component system signaling networks provides a strategy to study bacterial signaling mechanisms related to bacterial cell survival, symbiosis, and virulence, and to develop sensory devices in synthetic biology. Here we focus on the principles for engineering the HK to identify unknown signal inputs, test signal transmission mechanisms, design small molecule sensors, and rewire two-component signaling networks.
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Affiliation(s)
| | - Samuel W Duvall
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wei Zhao
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - W Seth Childers
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA. .,Chevron Science Center, University of Pittsburgh, Pittsburgh, PA, USA.
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12
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Agrobacterium-mediated horizontal gene transfer: Mechanism, biotechnological application, potential risk and forestalling strategy. Biotechnol Adv 2018; 37:259-270. [PMID: 30579929 DOI: 10.1016/j.biotechadv.2018.12.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 12/18/2018] [Accepted: 12/18/2018] [Indexed: 11/20/2022]
Abstract
The extraordinary capacity of Agrobacterium to transfer its genetic material to host cell makes it evolve from phytopathogen to a powerful transgenic vector. Agrobacterium-mediated stable transformation is widely used as the preferred method to create transgenic plants for molecular plant biology research and crop breeding. Recent years, both mechanism and application of Agrobacterium-mediated horizontal gene transfer have made significant progresses, especially Agrobacterium-mediated transient transformation was developed for plant biotechnology industry to produce recombinant proteins. Agrobacterium strains are almost used and saved not only by each of microbiology and molecular plant labs, but also by many of plant biotechnology manufacturers. Agrobacterium is able to transfer its genetic material to a broad range of hosts, including plant and non-plant hosts. As a consequence, the concern of environmental risk associated with the accidental release of genetically modified Agrobacterium arises. In this article, we outline the recent progress in the molecular mechanism of Agrobacterium-meditated gene transfer, focus on the application of Agrobacterium-mediated horizontal gene transfer, and review the potential risk associated with Agrobacterium-meditated gene transfer. Based on the comparison between the infecting process of Agrobacterium as a pathogen and the transgenic process of Agrobacterium as a transgenic vector, we realize that chemotaxis is the distinct difference between these two biological processes and thus discuss the possible role of chemotaxis in forestalling the potential risk of Agrobacterium-meditated horizontal gene transfer to non-target plant species.
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13
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Guo M, Huang Z, Yang J. Is there any crosstalk between the chemotaxis and virulence induction signaling in Agrobacterium tumefaciens? Biotechnol Adv 2017; 35:505-511. [PMID: 28342941 DOI: 10.1016/j.biotechadv.2017.03.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 03/17/2017] [Accepted: 03/22/2017] [Indexed: 12/25/2022]
Abstract
Agrobacterium tumefaciens, a soil-born phytopathogenic bacterium, is well known as a nature's engineer due to its ability to genetically transform the host by transferring a DNA fragment (called T-DNA) from its Ti plasmid to host-cell genome. To combat the harsh soil environment and seek the appropriate host, A. tumefaciens can sense and be attracted by a large number of chemical compounds released by wounded host. As a member of α-proteobacterium, A. tumefaciens has a chemotaxis system different from that found in Escherichia coli, since many chemoattractants for A. tumefaciens chemotaxis are virulence (vir) inducers. However, advances in the study of the chemotaxis paradigm, E. coli chemotaxis system, have provided enough information to analyze the A. tumefaciens chemotaxis. At low concentration, chemoattractants elicit A. tumefaciens chemotaxis and attract the species to the wound sites of the host. At high concentration, chemoattractants induce the expression of virulence genes and trigger T-DNA transfer. Recent studies on the VirA and ChvE of the vir-induction system provide some evidences to support the crosstalk between chemotaxis and vir-induction. This review compares the core components of chemotaxis signaling system of A. tumefaciens with those observed in other species, discusses the connection between chemotaxis and vir-induction in A. tumefaciens, and proposes a model depicting the signaling crosstalk between chemotaxis and vir-induction.
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Affiliation(s)
- Minliang Guo
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Zhiwei Huang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Jing Yang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, China
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14
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Mann TH, Seth Childers W, Blair JA, Eckart MR, Shapiro L. A cell cycle kinase with tandem sensory PAS domains integrates cell fate cues. Nat Commun 2016; 7:11454. [PMID: 27117914 PMCID: PMC4853435 DOI: 10.1038/ncomms11454] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 03/22/2016] [Indexed: 11/11/2022] Open
Abstract
All cells must integrate sensory information to coordinate developmental events in space and time. The bacterium Caulobacter crescentus uses two-component phospho-signalling to regulate spatially distinct cell cycle events through the master regulator CtrA. Here, we report that CckA, the histidine kinase upstream of CtrA, employs a tandem-PAS domain sensor to integrate two distinct spatiotemporal signals. Using CckA reconstituted on liposomes, we show that one PAS domain modulates kinase activity in a CckA density-dependent manner, mimicking the stimulation of CckA kinase activity that occurs on its transition from diffuse to densely packed at the cell poles. The second PAS domain interacts with the asymmetrically partitioned second messenger cyclic-di-GMP, inhibiting kinase activity while stimulating phosphatase activity, consistent with the selective inactivation of CtrA in the incipient stalked cell compartment. The integration of these spatially and temporally regulated signalling events within a single signalling receptor enables robust orchestration of cell-type-specific gene regulation. The membrane-bound kinase CckA controls the activity of the Caulobacter crescentus master regulator CtrA, which in turn coordinates asymmetric cell division. Here, the authors show that CckA contains two sensory domains that have distinct sensitivities to fluctuations in cyclic-di-GMP concentration and subcellular niche.
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Affiliation(s)
- Thomas H Mann
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - W Seth Childers
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jimmy A Blair
- Department of Chemistry, Williams College, Williamstown, Massachusetts 01267, USA
| | - Michael R Eckart
- Stanford Protein and Nucleic Acid Facility, Beckman Center, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
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15
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Czarnecka-Verner E, Salem TA, Gurley WB. Adaptation of the Agrobacterium tumefaciens VirG response regulator to activate transcription in plants. PLANT MOLECULAR BIOLOGY 2016; 90:217-31. [PMID: 26646288 DOI: 10.1007/s11103-015-0407-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 11/11/2015] [Indexed: 06/05/2023]
Abstract
The Agrobacterium tumefaciens VirG response regulator of the VirA/VirG two-component system was adapted to function in tobacco protoplasts. The subcellular localization of VirG and VirA proteins transiently expressed in onion cells was determined using GFP fusions. Preliminary studies using Gal4DBD-VP16 fusions with VirG and Escherichia coli UhpA, and NarL response regulators indicated compatibility of these bacterial proteins with the eukaryotic transcriptional apparatus. A strong transcriptional activator based on tandem activation domains from the Drosophila fushi tarazu and Herpes simplex VP16 was created. Selected configurations of the two-site Gal4-vir box GUS reporters were activated by chimeric effectors dependent on either the yeast Gal4 DNA-binding domain or that of VirG. Transcriptional induction of the GUS reporter was highest for the VirE19-element promoter with both constitutive and wild-type VirG-tandem activation domain effectors. Multiple VirE19 elements increased the reporter activity proportionately, indicating that the VirG DNA binding domain was functional in plants. The VirG constitutive-Q-VP16 effector was more active than the VirG wild-type. In both the constitutive and wild-type forms of VirG, Q-VP16 activated transcription of the GUS reporter best when located at the C-terminus, i.e. juxtaposed to the VirG DNA binding domain. These results demonstrate the possibility of using DNA binding domains from bacterial response regulators and their cognate binding elements in the engineering of plant gene expression.
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Affiliation(s)
- Eva Czarnecka-Verner
- Department of Microbiology and Cell Science, Program of Plant Molecular and Cellular Biology, University of Florida, Bldg. 981, 1355 Museum Drive, P.O. Box 110700, Gainesville, FL, 32611-0700, USA.
| | - Tarek A Salem
- Department of Microbiology and Cell Science, Program of Plant Molecular and Cellular Biology, University of Florida, Bldg. 981, 1355 Museum Drive, P.O. Box 110700, Gainesville, FL, 32611-0700, USA
- Molecular Biology Department, Genetic Engineering and Biotechnology Institute, University of Sadat City, Sadat City, Egypt
| | - William B Gurley
- Department of Microbiology and Cell Science, Program of Plant Molecular and Cellular Biology, University of Florida, Bldg. 981, 1355 Museum Drive, P.O. Box 110700, Gainesville, FL, 32611-0700, USA.
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16
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Wise AA, Binns AN. The Receiver of the Agrobacterium tumefaciens VirA Histidine Kinase Forms a Stable Interaction with VirG to Activate Virulence Gene Expression. Front Microbiol 2016; 6:1546. [PMID: 26779177 PMCID: PMC4705274 DOI: 10.3389/fmicb.2015.01546] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 12/21/2015] [Indexed: 01/20/2023] Open
Abstract
The plant pathogen Agrobacterium tumefaciens carries a virulence gene system that is required for the initiation of crown gall tumors on susceptible plants. Expression of the vir genes is activated by the VirA/VirG two component regulatory system. VirA is a histidine kinase which signals the presence of certain chemicals found at the site of a plant wound. The receiver domain located at its carboxyl terminus defines VirA as a hybrid histidine kinase. Here, we show that the VirA receiver interacts with the DNA-binding domain of VirG. This finding supports the hypothesis that the receiver acts as a recruiting factor for VirG. In addition, we show that removal of the VirA receiver allowed vir gene expression in response to glucose in a dose dependent manner, indicating that the receiver controls VirG activation and suggesting that the supplementary ChvE-sugar signal increases this activity.
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Affiliation(s)
- Arlene A Wise
- Binns Lab, Department of Biology, University of Pennsylvania, Philadelphia PA, USA
| | - Andrew N Binns
- Binns Lab, Department of Biology, University of Pennsylvania, Philadelphia PA, USA
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17
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Chen JC, Liu JH, Hsu DW, Shu JC, Chen CY, Chen CC. Methylatable Signaling Helix Coordinated Inhibitory Receiver Domain in Sensor Kinase Modulates Environmental Stress Response in Bacillus Cereus. PLoS One 2015; 10:e0137952. [PMID: 26379238 PMCID: PMC4574943 DOI: 10.1371/journal.pone.0137952] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/25/2015] [Indexed: 02/08/2023] Open
Abstract
σB, an alternative transcription factor, controls the response of the cell to a variety of environmental stresses in Bacillus cereus. Previously, we reported that RsbM negatively regulates σB through the methylation of RsbK, a hybrid sensor kinase, on a signaling helix (S-helix). However, RsbK comprises a C-terminal receiver (REC) domain whose function remains unclear. In this study, deletion of the C-terminal REC domain of RsbK resulted in high constitutive σB expression independent of environmental stimuli. Thus, the REC domain may serve as an inhibitory element. Mutagenic substitution was employed to modify the putative phospho-acceptor residue D827 in the REC domain of RsbK. The expression of RsbKD827N and RsbKD827E exhibited high constitutive σB, indicating that D827, if phosphorylatable, possibly participates in σB regulation. Bacterial two-hybrid analyses demonstrated that RsbK forms a homodimer and the REC domain interacts mainly with the histidine kinase (HK) domain and partly with the S-helix. In particular, co-expression of RsbM strengthens the interaction between the REC domain and the S-helix. Consistently, our structural model predicts a significant interaction between the HK and REC domains of the RsbK intradimer. Here, we demonstrated that coordinated the methylatable S-helix and the REC domain of RsbK is functionally required to modulate σB-mediated stress response in B. cereus and maybe ubiquitous in microorganisms encoded RsbK-type sensor kinases.
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Affiliation(s)
- Jung-Chi Chen
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
| | - Jyung-Hurng Liu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
- Agricultural Biotechnology Center (ABC), National Chung Hsing University, Taichung, Taiwan
| | - Duen-Wei Hsu
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
| | - Jwu-Ching Shu
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Tao-Yuan, Taiwan
| | - Chien-Yen Chen
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Chien-Cheng Chen
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
- * E-mail:
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18
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Bhate MP, Molnar KS, Goulian M, DeGrado WF. Signal transduction in histidine kinases: insights from new structures. Structure 2015; 23:981-94. [PMID: 25982528 DOI: 10.1016/j.str.2015.04.002] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 03/22/2015] [Accepted: 03/30/2015] [Indexed: 10/23/2022]
Abstract
Histidine kinases (HKs) are major players in bacterial signaling. There has been an explosion of new HK crystal structures in the last 5 years. We globally analyze the structures of HKs to yield insights into the mechanisms by which signals are transmitted to and across protein structures in this family. We interpret known enzymological data in the context of new structural data to show how asymmetry across the dimer interface is a key feature of signal transduction in HKs, and discuss how different HK domains undergo asymmetric to symmetric transitions during signal transduction and catalysis. A thermodynamic framework for signaling that encompasses these various properties is presented, and the consequences of weak thermodynamic coupling are discussed. The synthesis of observations from enzymology, structural biology, protein engineering, and thermodynamics paves the way for a deeper molecular understanding of HK signal transduction.
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Affiliation(s)
- Manasi P Bhate
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, 555 Mission Bay Boulevard South, Box 3122, San Francisco, CA 94158, USA
| | - Kathleen S Molnar
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, 555 Mission Bay Boulevard South, Box 3122, San Francisco, CA 94158, USA; Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mark Goulian
- Department of Biology and Department of Physics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, 555 Mission Bay Boulevard South, Box 3122, San Francisco, CA 94158, USA.
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19
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Hwang HH, Gelvin SB, Lai EM. Editorial: "Agrobacterium biology and its application to transgenic plant production". FRONTIERS IN PLANT SCIENCE 2015; 6:265. [PMID: 25954291 PMCID: PMC4406079 DOI: 10.3389/fpls.2015.00265] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 04/02/2015] [Indexed: 05/15/2023]
Affiliation(s)
- Hau-Hsuan Hwang
- Department of Life Sciences, National Chung Hsing UniversityTaichung, Taiwan
- *Correspondence: Hau-Hsuan Hwang,
| | - Stanton B. Gelvin
- Department of Biological Sciences, Purdue UniversityWest Lafayette, IN, USA
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia SinicaTaipei, Taiwan
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20
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Shalaby S, Horwitz BA. Plant phenolic compounds and oxidative stress: integrated signals in fungal-plant interactions. Curr Genet 2014; 61:347-57. [PMID: 25407462 DOI: 10.1007/s00294-014-0458-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 10/17/2014] [Accepted: 10/21/2014] [Indexed: 01/09/2023]
Abstract
Upon invasion of a host, fungal pathogens are exposed to a variety of stresses. Plants release reactive oxygen species, and mount a variety of preformed and induced chemical defenses. Phenolic compounds are one example: they are ubiquitous in plants, and an invading pathogen encounters them already at the leaf surface, or for soil-borne pathogens, in the rhizosphere. Phenolic and related aromatic compounds show varying degrees of toxicity to cells. Some compounds are quite readily metabolized, and others less so. It was known already from classical studies that phenolic substrates induce the expression of the enzymes for their degradation. Recently, the ability to degrade phenolics was shown to be a virulence factor. Conversely, phenolic compounds can increase the effectiveness of antifungals. Phenolics are known antioxidants, yet they have been shown to elicit cellular responses that would usually be triggered to counter oxidant stress. Here, we review the evidence for a connection between the fungal response to phenolics as small-molecule signals, and the response to oxidants. The connections proposed here should enable genetic screens to identify specific fungal receptors for plant phenolics. Furthermore, understanding how the pathogen detects plant phenolic compounds as a stress signal may facilitate new antifungal strategies.
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Affiliation(s)
- Samer Shalaby
- Department of Biology, Technion, Israel Institute of Technology, 3200000, Haifa, Israel
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21
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Cell fate regulation governed by a repurposed bacterial histidine kinase. PLoS Biol 2014; 12:e1001979. [PMID: 25349992 PMCID: PMC4211667 DOI: 10.1371/journal.pbio.1001979] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 09/17/2014] [Indexed: 11/19/2022] Open
Abstract
The pathway that regulates asymmetric cell division in Caulobacter involves a signaling kinase whose catalytic output domain has been repurposed as an input sensor of the phosphorylation state of the response regulator – a reversal of the conventional direction of information flow; this allows wiring of simple linear signaling pathways into complex eukaryote-like networks. One of the simplest organisms to divide asymmetrically is the bacterium Caulobacter crescentus. The DivL pseudo-histidine kinase, positioned at one cell pole, regulates cell-fate by controlling the activation of the global transcription factor CtrA via an interaction with the response regulator (RR) DivK. DivL uniquely contains a tyrosine at the histidine phosphorylation site, and can achieve these regulatory functions in vivo without kinase activity. Determination of the DivL crystal structure and biochemical analysis of wild-type and site-specific DivL mutants revealed that the DivL PAS domains regulate binding specificity for DivK∼P over DivK, which is modulated by an allosteric intramolecular interaction between adjacent domains. We discovered that DivL's catalytic domains have been repurposed as a phosphospecific RR input sensor, thereby reversing the flow of information observed in conventional histidine kinase (HK)-RR systems and coupling a complex network of signaling proteins for cell-fate regulation. Across all kingdoms of life the generation of cell-type diversity is the consequence of asymmetry at the point of cell division. The bacterium Caulobacter crescentus divides asymmetrically to produce daughter cells that have distinct morphology and behavior. As in eukaryotes, an unequal distribution of signaling proteins in daughter Caulobacter cells triggers the differential read-out of identical genomes. A critical interaction between two protein molecules – a protein kinase (DivL) and a response regulator (DivK) – is known to occur exclusively in one daughter cell and to thereby regulate differentiation. However, mapping the observed signaling interconnections that drive asymmetric division has been difficult to reconcile with traditional models of bacterial signaling. Here we determine how DivL detects and processes this DivK signal. Although DivL has an architecture that is typical of histidine kinases, which normally act by regulating the phosphorylation state of the appropriate response regulator, DivL's essential functions do not require kinase activity and DivL does not add or remove phosphate from DivK. Instead we find that DivL has converted its output kinase domain into an input sensor domain that specifically detects phosphorylated DivK, and we identify key features of DivL that underlie this specificity. This novel reassignment of sensory functions reverses the conventional kinase-to-response-regulator signaling flow and logically couples linear signaling pathways into complex eukaryote-like networks to regulate cell development.
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