Unravelling the Initial Triggers of Botrytis cinerea Infection: First Description of Its Surfactome

Botrytis cinerea is a critically important phytopathogenic fungus, causing devastating crop losses; signal transduction cascades mediate the “dialogue” among the fungus, plant, and environment. Surface proteins play important roles as front-line receptors. We report the first description of the surfactome of a filamentous fungus. To obtain a complete view of these cascades during infection of B. cinerea, its surfactome has been described by optimization of the “shaving” process and LC–MS/MS at two different infection stages, and with both rapid and late responses to environmental changes. The best results were obtained using PBS buffer in the “shaving” protocol. The surfactome obtained comprises 1010 identified proteins. These have been categorized by gene ontology and protein–protein interactions to reveal new potential pathogenicity/virulence factors. From these data, the percentage of total proteins predicted for the genome of the fungus represented by proteins identified in this and other proteomics studies is calculated at 54%, a big increase over the previous 12%. The new data may be crucial for understanding better its biological activity and pathogenicity. Given its extensive exposure to plants and environmental conditions, the surfactome presents innumerable opportunities for interactions between the fungus and external elements, which should offer the best targets for fungicide development.

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Phyletic Distribution and Lineage-Specific Domain Architectures of Archaeal Two-Component Signal Transduction Systems

Journal of Bacteriology ◽

10.1128/jb.00681-17 ◽

2017 ◽

Vol 200 (7) ◽

Cited By ~ 8

Author(s):

Michael Y. Galperin ◽

Kira S. Makarova ◽

Yuri I. Wolf ◽

Eugene V. Koonin

Keyword(s):

Signal Transduction ◽

Protein Interactions ◽

Environmental Changes ◽

Metagenomic Data ◽

Protein Protein Interactions ◽

Response Regulators ◽

Histidine Kinases ◽

Content Type ◽

Two Component ◽

Two Component Signal Transduction

ABSTRACTThe two-component signal transduction (TCS) machinery is a key mechanism of sensing environmental changes in the prokaryotic world. TCS systems have been characterized thoroughly in bacteria but to a much lesser extent in archaea. Here, we provide an updated census of more than 2,000 histidine kinases and response regulators encoded in 218 complete archaeal genomes, as well as unfinished genomes available from metagenomic data. We describe the domain architectures of the archaeal TCS components, including several novel output domains, and discuss the evolution of the archaeal TCS machinery. The distribution of TCS systems in archaea is strongly biased, with high levels of abundance in haloarchaea and thaumarchaea but none detected in the sequenced genomes from the phylaCrenarchaeota,Nanoarchaeota, andKorarchaeota. The archaeal sensor histidine kinases are generally similar to their well-studied bacterial counterparts but are often located in the cytoplasm and carry multiple PAS and/or GAF domains. In contrast, archaeal response regulators differ dramatically from the bacterial ones. Most archaeal genomes do not encode any of the major classes of bacterial response regulators, such as the DNA-binding transcriptional regulators of the OmpR/PhoB, NarL/FixJ, NtrC, AgrA/LytR, and ActR/PrrA families and the response regulators with GGDEF and/or EAL output domains. Instead, archaea encode multiple copies of response regulators containing either the stand-alone receiver (REC) domain or combinations of REC with PAS and/or GAF domains. Therefore, the prevailing mechanism of archaeal TCS signaling appears to be via a variety of protein-protein interactions, rather than direct transcriptional regulation.IMPORTANCEAlthough theArchaearepresent a separate domain of life, their signaling systems have been assumed to be closely similar to the bacterial ones. A study of the domain architectures of the archaeal two-component signal transduction (TCS) machinery revealed an overall similarity of archaeal and bacterial sensory modules but substantial differences in the signal output modules. The prevailing mechanism of archaeal TCS signaling appears to involve various protein-protein interactions rather than direct transcription regulation. The complete list of histidine kinases and response regulators encoded in the analyzed archaeal genomes is available online athttp://www.ncbi.nlm.nih.gov/Complete_Genomes/TCSarchaea.html.

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Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism

Nature Communications ◽

10.1038/s41467-021-22253-6 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Christopher R. Horne ◽

Hariprasad Venugopal ◽

Santosh Panjikar ◽

David M. Wood ◽

Amy Henrickson ◽

...

Keyword(s):

Sialic Acid ◽

Dna Binding ◽

Protein Interactions ◽

Acid Metabolism ◽

Environmental Changes ◽

Dna Interaction ◽

Protein Protein Interactions ◽

Nutrient Source ◽

Cryo Electron Microscopy ◽

Close Proximity

AbstractBacteria respond to environmental changes by inducing transcription of some genes and repressing others. Sialic acids, which coat human cell surfaces, are a nutrient source for pathogenic and commensal bacteria. The Escherichia coli GntR-type transcriptional repressor, NanR, regulates sialic acid metabolism, but the mechanism is unclear. Here, we demonstrate that three NanR dimers bind a (GGTATA)3-repeat operator cooperatively and with high affinity. Single-particle cryo-electron microscopy structures reveal the DNA-binding domain is reorganized to engage DNA, while three dimers assemble in close proximity across the (GGTATA)3-repeat operator. Such an interaction allows cooperative protein-protein interactions between NanR dimers via their N-terminal extensions. The effector, N-acetylneuraminate, binds NanR and attenuates the NanR-DNA interaction. The crystal structure of NanR in complex with N-acetylneuraminate reveals a domain rearrangement upon N-acetylneuraminate binding to lock NanR in a conformation that weakens DNA binding. Our data provide a molecular basis for the regulation of bacterial sialic acid metabolism.

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POT1-TPP1 differentially regulates telomerase via POT1 His266 and as a function of single-stranded telomere DNA length

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1905381116 ◽

2019 ◽

Vol 116 (47) ◽

pp. 23527-23533 ◽

Cited By ~ 9

Author(s):

Mengyuan Xu ◽

Janna Kiselar ◽

Tawna L. Whited ◽

Wilnelly Hernandez-Sanchez ◽

Derek J. Taylor

Keyword(s):

Conformational Changes ◽

Protein Interactions ◽

Environmental Changes ◽

Lymphocytic Leukemia ◽

Protein Protein Interactions ◽

Cellular Environment ◽

Multiple Protein ◽

Linear Chromosomes ◽

Hydroxyl Radical Footprinting ◽

Regulate Telomere Length

Telomeres cap the ends of linear chromosomes and terminate in a single-stranded DNA (ssDNA) overhang recognized by POT1-TPP1 heterodimers to help regulate telomere length homeostasis. Here hydroxyl radical footprinting coupled with mass spectrometry was employed to probe protein–protein interactions and conformational changes involved in the assembly of telomere ssDNA substrates of differing lengths bound by POT1-TPP1 heterodimers. Our data identified environmental changes surrounding residue histidine 266 of POT1 that were dependent on telomere ssDNA substrate length. We further determined that the chronic lymphocytic leukemia-associated H266L substitution significantly reduced POT1-TPP1 binding to short ssDNA substrates; however, it only moderately impaired the heterodimer binding to long ssDNA substrates containing multiple protein binding sites. Additionally, we identified a telomerase inhibitory role when several native POT1-TPP1 proteins coat physiologically relevant lengths of telomere ssDNA. This POT1-TPP1 complex-mediated inhibition of telomerase is abrogated in the context of the POT1 H266L mutation, which leads to telomere overextension in a malignant cellular environment.

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Properties of the phage-shock-protein (Psp) regulatory complex that govern signal transduction and induction of the Psp response in Escherichia coli

Microbiology ◽

10.1099/mic.0.040055-0 ◽

2010 ◽

Vol 156 (10) ◽

pp. 2920-2932 ◽

Cited By ~ 29

Author(s):

Goran Jovanovic ◽

Christoph Engl ◽

Antony J. Mayhew ◽

Patricia C. Burrows ◽

Martin Buck

Keyword(s):

Escherichia Coli ◽

Signal Transduction ◽

Protein Interactions ◽

Leucine Zipper ◽

Negative Control ◽

Stress Conditions ◽

Bacterial Cells ◽

Protein Protein Interactions ◽

Regulatory Complex ◽

And Function

The phage-shock-protein (Psp) response maintains the proton-motive force (pmf) under extracytoplasmic stress conditions that impair the inner membrane (IM) in bacterial cells. In Escherichia coli transcription of the pspABCDE and pspG genes requires activation of σ 54-RNA polymerase by the enhancer-binding protein PspF. A regulatory network comprising PspF–A–C–B–ArcB controls psp expression. One key regulatory point is the negative control of PspF imposed by its binding to PspA. It has been proposed that under stress conditions, the IM-bound sensors PspB and PspC receive and transduce the signal(s) to PspA via protein–protein interactions, resulting in the release of the PspA–PspF inhibitory complex and the consequent induction of psp. In this work we demonstrate that PspB self-associates and interacts with PspC via putative IM regions. We present evidence suggesting that PspC has two topologies and that conserved residue G48 and the putative leucine zipper motif are determinants required for PspA interaction and signal transduction upon stress. We also establish that PspC directly interacts with the effector PspG, and show that PspG self-associates. These results are discussed in the context of formation and function of the Psp regulatory complex.

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Protein-Protein Interactions in the Tetraspanin Web

Physiology ◽

10.1152/physiol.00015.2005 ◽

2005 ◽

Vol 20 (4) ◽

pp. 218-224 ◽

Cited By ~ 132

Author(s):

Shoshana Levy ◽

Tsipi Shoham

Keyword(s):

Signal Transduction ◽

Cell Proliferation ◽

Protein Interactions ◽

Membrane Microdomains ◽

Protein Protein Interactions ◽

Host Parasite Interactions ◽

Evolutionarily Conserved ◽

And Migration ◽

Host Parasite ◽

Partner Proteins

Tetraspanins are evolutionarily conserved membrane proteins that tend to associate laterally with one another and to cluster dynamically with numerous partner proteins in membrane microdomains. Consequently, members of this family are involved in the coordination of intracellular and intercellular processes, including signal transduction; cell proliferation, adhesion, and migration; cell fusion; and host-parasite interactions.

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The road less traveled: modulating signal transduction enzymes by inhibiting their protein–protein interactions

Current Opinion in Chemical Biology ◽

10.1016/j.cbpa.2009.05.125 ◽

2009 ◽

Vol 13 (3) ◽

pp. 284-290 ◽

Cited By ~ 124

Author(s):

Michelle R Arkin ◽

Adrian Whitty

Keyword(s):

Signal Transduction ◽

Protein Interactions ◽

Protein Protein Interactions ◽

The Road

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Src homology region 2 domains direct protein-protein interactions in signal transduction.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.87.21.8622 ◽

1990 ◽

Vol 87 (21) ◽

pp. 8622-8626 ◽

Cited By ~ 243

Author(s):

M. F. Moran ◽

C. A. Koch ◽

D. Anderson ◽

C. Ellis ◽

L. England ◽

...

Keyword(s):

Signal Transduction ◽

Protein Interactions ◽

Protein Protein Interactions ◽

Homology Region ◽

Src Homology

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Interactions of bacterial cell-surface proteins with antibodies: a ersatile set of protein-protein interactions

Techniques in Protein Chemistry ◽

10.1016/s1080-8914(06)80050-5 ◽

1995 ◽

pp. 409-416 ◽

Cited By ~ 1

Author(s):

Gordon C.K. Roberts ◽

Lu-Yun Lian ◽

Igor L. Barsukov ◽

Jeremy P. Derrick ◽

Koichi Kato ◽

...

Keyword(s):

Cell Surface ◽

Protein Interactions ◽

Bacterial Cell ◽

Surface Proteins ◽

Protein Protein Interactions ◽

Cell Surface Proteins ◽

Bacterial Cell Surface

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Prediction of the Secretome and the Surfaceome: A Strategy to Decipher the Crosstalk between Adipose Tissue and Muscle during Fetal Growth

International Journal of Molecular Sciences ◽

10.3390/ijms21124375 ◽

2020 ◽

Vol 21 (12) ◽

pp. 4375

Author(s):

Muriel Bonnet ◽

Nicolas Kaspric ◽

Kimberly Vonnahme ◽

Didier Viala ◽

Christophe Chambon ◽

...

Keyword(s):

Adipose Tissue ◽

Cell Surface ◽

Fetal Growth ◽

Protein Interactions ◽

Cell Types ◽

Surface Proteins ◽

Protein Protein Interactions ◽

Cell Surface Proteins ◽

Bovine Fetuses ◽

Muscular Tissues

Crosstalk between adipose and muscular tissues is hypothesized to regulate the number of muscular and adipose cells during fetal growth, with post-natal consequences on lean and fat masses. Such crosstalk largely remains, however, to be described. We hypothesized that a characterization of the proteomes of adipose and muscular tissues from bovine fetuses may enhance the understanding of the crosstalk between these tissues through the prediction of their secretomes and surfaceomes. Proteomic experiments have identified 751 and 514 proteins in fetal adipose tissue and muscle. These are mainly involved in the regulation of cell proliferation or differentiation, but also in pathways such as apoptosis, Wnt signalling, or cytokine-mediated signalling. Of the identified proteins, 51 adipokines, 11 myokines, and 37 adipomyokines were predicted, together with 26 adipose and 13 muscular cell surface proteins. Analysis of protein–protein interactions suggested 13 links between secreted and cell surface proteins that may contribute to the adipose–muscular crosstalk. Of these, an interaction between the adipokine plasminogen and the muscular cell surface alpha-enolase may regulate the fetal myogenesis. The in silico secretome and surfaceome analyzed herein exemplify a powerful strategy to enhance the elucidation of the crosstalk between cell types or tissues.

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