The structural repertoire of Fusarium oxysporum f. sp. lycopersici effectors revealed by experimental and computational studies

2021 ◽  
Author(s):  
Daniel S. Yu ◽  
Megan A Outram ◽  
Ashley Smith ◽  
Carl L McCombe ◽  
Pravin B Khambalkar ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Structure Prediction ◽  
Plant Pathogens ◽  
Plant Immunity ◽  
Sequence Motifs ◽  
Structural Class ◽  
X Ray Crystallography ◽  
Pathogen Virulence ◽  
Plant Infection ◽  
Dual Domain

Plant pathogens secrete proteins, known as effectors, that function in the apoplast and inside plant cells to promote virulence. Effectors can also be detected by cell-surface and cytosolic receptors, resulting in the activation of defence pathways and plant immunity. Our understanding of fungal effector function and detection by immunity receptors is limited largely due to high sequence diversity and lack of identifiable sequence motifs precluding prediction of structure or function. Recent studies have demonstrated that fungal effectors can be grouped into structural classes despite significant sequence variation. Using protein x-ray crystallography, we identify a new structural class of effectors hidden within the secreted in xylem (SIX) effectors from Fusarium oxysporum f. sp. lycopersici (Fol). The recognised effectors Avr1 (SIX4) and Avr3 (SIX1) represent the founding members of the Fol dual-domain (FOLD) effector class. Using AlphaFold ab initio protein structure prediction, benchmarked against the experimentally determined structures, we demonstrate SIX6 and SIX13 are FOLD effectors. We show that the conserved N-domain of Avr1 and Avr3 is sufficient for recognition by their corresponding, but structurally-distinct, immunity receptors. Additional structural prediction and comparison indicate that 11 of the 14 SIX effectors group into four structural families. This revealed that genetically linked effectors are related structurally, and we provide direct evidence for a physical association between one divergently-transcribed effector pair. Collectively, these data indicate that Fol secretes groups of structurally-related molecules during plant infection, an observation that has broad implications for our understanding of pathogen virulence and the engineering of plant immunity receptors.

scholarly journals Motif Discovery in Protein Structure Databases

1999 ◽  
Author(s):  
Janice Glasgow ◽  
Evan Steeg
Keyword(s):  
Protein Structure ◽  
Protein Sequence ◽  
Structure Prediction ◽  
Sequence Motifs ◽  
Computational Molecular Biology ◽  
X Ray ◽  
X Ray Crystallography ◽  
Efficiency And Effectiveness ◽  
Structure Prediction Program ◽  
Automated Discovery

The field of knowledge discovery is concerned with the theory and processes involved in the representation and extraction of patterns or motifs from large databases. Discovered patterns can be used to group data into meaningful classes, to summarize data, or to reveal deviant entries. Motifs stored in a database can be brought to bear on difficult instances of structure prediction or determination from X-ray crystallography or nuclear magnetic resonance (NMR) experiments. Automated discovery techniques are central to understanding and analyzing the rapidly expanding repositories of protein sequence and structure data. This chapter deals with the discovery of protein structure motifs. A motif is an abstraction over a set of recurring patterns observed in a dataset; it captures the essential features shared by a set of similar or related objects. In many domains, such as computer vision and speech recognition, there exist special regularities that permit such motif abstraction. In the protein science domain, the regularities derive from evolutionary and biophysical constraints on amino acid sequences and structures. The identification of a known pattern in a new protein sequence or structure permits the immediate retrieval and application of knowledge obtained from the analysis of other proteins. The discovery and manipulation of motifs—in DNA, RNA, and protein sequences and structures—is thus an important component of computational molecular biology and genome informatics. In particular, identifying protein structure classifications at varying levels of abstraction allows us to organize and increase our understanding of the rapidly growing protein structure datasets. Discovered motifs are also useful for improving the efficiency and effectiveness of X-ray crystallographic studies of proteins, for drug design, for understanding protein evolution, and ultimately for predicting the structure of proteins from sequence data. Motifs may be designed by hand, based on expert knowledge. For example, the Chou-Fasman protein secondary structure prediction program (Chou and Fasman, 1978), which dominated the field for many years, depended on the recognition of predefined, user-encoded sequence motifs for α-helices and β-sheets. Several hundred sequence motifs have been cataloged in PROSITE (Bairoch, 1992); the identification of one of these motifs in a novel protein often allows for immediate function interpretation.

scholarly journals Host–Pathogen Interaction in Fusarium oxysporum Infections: Where Do We Stand?

2018 ◽  
Vol 31 (9) ◽  
pp. 889-898 ◽  
Author(s):  
Amjad M. Husaini ◽  
Aafreen Sakina ◽  
Souliha R. Cambay
Keyword(s):  
Fusarium Oxysporum ◽  
Plant Pathogens ◽  
Molecular Mechanisms ◽  
Plant Immunity ◽  
Mitogen Activated Protein Kinase ◽  
Signal Pathways ◽  
Protein Signaling ◽  
Host Interactions ◽  
Fungal Plant Pathogens ◽  
Mitogen Activated Protein

Fusarium oxysporum, a ubiquitous soilborne pathogen, causes devastating vascular wilt in more than 100 plant species and ranks 5th among the top 10 fungal plant pathogens. It has emerged as a human pathogen, too, causing infections in immune-compromised patients. Therefore, it is important to gain insight into the molecular processes involved in the pathogenesis of this transkingdom pathogen. A complex network comprising interconnected and overlapping signal pathways—mitogen-activated protein kinase signaling pathways, Ras proteins, G-protein signaling components and their downstream pathways, components of the velvet (LaeA/VeA/VelB) complex, and cAMP pathways—is involved in perceiving the host. This network regulates the expression of various pathogenicity genes. However, plants have evolved an elaborate protection system to combat this attack. They, too, possess intricate mechanisms at the molecular level which, once triggered by pathogen attack, transduce signals to activate defense response. This review focuses on understanding and presenting a wholistic picture of the molecular mechanisms of F. oxysporum–host interactions in plant immunity.

scholarly journals In planta bacterial multi-omics analysis illuminates regulatory principles underlying plant-pathogen interactions

2019 ◽  
Author(s):  
Tatsuya Nobori ◽  
Yiming Wang ◽  
Jingni Wu ◽  
Sara Christina Stolze ◽  
Yayoi Tsuda ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Pseudomonas Syringae ◽  
Protein Level ◽  
Plant Pathogens ◽  
Plant Immunity ◽  
Bacterial Pathogen ◽  
Bacterial Virulence ◽  
In Planta ◽  
Bacterial Gene ◽  
Global Food Security

AbstractUnderstanding how gene expression is regulated in plant pathogens is crucial for pest control and thus global food security. An integrated understanding of bacterial gene regulation in the host is dependent on multi-omic datasets, but these are largely lacking. Here, we simultaneously characterized the transcriptome and proteome of a foliar bacterial pathogen, Pseudomonas syringae, in Arabidopsis thaliana and identified a number of bacterial processes influenced by plant immunity at the mRNA and the protein level. We found instances of both concordant and discordant regulation of bacterial mRNAs and proteins. Notably, the tip component of bacterial type III secretion system was selectively suppressed by the plant salicylic acid pathway at the protein level, suggesting protein-level targeting of the bacterial virulence system by plant immunity. Furthermore, gene co-expression analysis illuminated previously unknown gene regulatory modules underlying bacterial virulence and their regulatory hierarchy. Collectively, the integrated in planta bacterial omics approach provides molecular insights into multiple layers of bacterial gene regulation that contribute to bacterial growth in planta and elucidate the role of plant immunity in controlling pathogens.

scholarly journals Using FIBexDB for In-Depth Analysis of Flax Lectin Gene Expression in Response to Fusarium oxysporum Infection

Plants ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 163
Author(s):  
Natalia Petrova ◽  
Natalia Mokshina
Keyword(s):  
Gene Expression ◽  
Fusarium Oxysporum ◽  
Essential Role ◽  
Protein Biosynthesis ◽  
Plant Immunity ◽  
Gene Clustering ◽  
Root Tips ◽  
Lectin Gene ◽  
Depth Analysis ◽  
Lectin Genes

Plant proteins with lectin domains play an essential role in plant immunity modulation, but among a plurality of lectins recruited by plants, only a few members have been functionally characterized. For the analysis of flax lectin gene expression, we used FIBexDB, which includes an efficient algorithm for flax gene expression analysis combining gene clustering and coexpression network analysis. We analyzed the lectin gene expression in various flax tissues, including root tips infected with Fusarium oxysporum. Two pools of lectin genes were revealed: downregulated and upregulated during the infection. Lectins with suppressed gene expression are associated with protein biosynthesis (Calreticulin family), cell wall biosynthesis (galactose-binding lectin family) and cytoskeleton functioning (Malectin family). Among the upregulated lectin genes were those encoding lectins from the Hevein, Nictaba, and GNA families. The main participants from each group are discussed. A list of lectin genes, the expression of which can determine the resistance of flax, is proposed, for example, the genes encoding amaranthins. We demonstrate that FIBexDB is an efficient tool both for the visualization of data, and for searching for the general patterns of lectin genes that may play an essential role in normal plant development and defense.

scholarly journals Characteristic of the bread wheat leaf rust pathogen virulence in the Saratov region conditions

2020 ◽  
pp. 40-44
Author(s):  
Sergey Nikolaevich Sibikeev ◽  
Elmira Alexandrovna Konkova ◽  
Maria Fedorovna Salmova
Keyword(s):  
Bread Wheat ◽  
Agricultural Research ◽  
Plant Immunity ◽  
Maximum Level ◽  
Partial Loss ◽  
Pathogen Virulence ◽  
Winter Bread Wheat ◽  
High Virulence ◽  
Wheat Leaf ◽  
Pathogen Populations

The studies were conducted in the Lababoratory of plant immunity Agricultural Research Institute for South-East Regions Russia.  The samples of pathogen populations were collected from commercial and promising cultivars of spring and winter bread wheat at the end of their growing season at the maximum level of disease development in a field nursery. Then this inoculum's has been propagated on susceptible cultivars of bread wheat in the laboratory conditions. During three years of studies (2017-2019) 30 monopustules isolates has been  studied. These studied isolates were avirulent to Thatcher near isogenic lines with genes Lr41, Lr42, Lr43+24, Lr53 and virulent to Lr1, Lr2a, Lr2b, Lr2c, Lr3, Lr3bg, Lr3ka, Lr10, Lr11, Lr12, Lr13, Lr14a, Lr14b, Lr15, Lr16, Lr17, Lr18, Lr21, lr22a, lr22b, lr25, lr28, LR 30, Lr32, Lr33, Lr34, Lr35, lr36, lr37, LR 38, Lr40, LR44, Lr45, LR b, LR W, LR Erph, LR Kanred, Lr57, Lr67. The significant variation for virulence was observed in lines with the Lr20, Lr23, Lr24, Lr26, Lr29, and Lr47 genes.  The study of the P. triticina population structure in 2017-2019 revealed a partial loss of the effectiveness of the Lr47 gene. It was found that populations of P. triticina in 2017-2019 were characterized by high virulence.

scholarly journals Bridging the Gap: Type III Secretion Systems in Plant-Beneficial Bacteria

2022 ◽  
Vol 10 (1) ◽  
pp. 187
Author(s):  
Antoine Zboralski ◽  
Adrien Biessy ◽  
Martin Filion
Keyword(s):  
Type Iii Secretion ◽  
Plant Pathogens ◽  
Plant Immunity ◽  
Effector Proteins ◽  
Secretion Systems ◽  
Beneficial Bacteria ◽  
Living Plant ◽  
Pseudomonas Spp ◽  
Type Iii ◽  
Type Iii Secretion Systems

Type III secretion systems (T3SSs) are bacterial membrane-embedded nanomachines translocating effector proteins into the cytoplasm of eukaryotic cells. They have been intensively studied for their important roles in animal and plant bacterial diseases. Over the past two decades, genome sequencing has unveiled their ubiquitous distribution in many taxa of Gram-negative bacteria, including plant-beneficial ones. Here, we discuss the distribution and functions of the T3SS in two agronomically important bacterial groups: the symbiotic nodule-forming nitrogen-fixing rhizobia and the free-living plant-beneficial Pseudomonas spp. In legume-rhizobia symbiosis, T3SSs and their cognate effectors play important roles, including the modulation of the plant immune response and the initiation of the nodulation process in some cases. In plant-beneficial Pseudomonas spp., the roles of T3SSs are not fully understood, but pertain to plant immunity suppression, biocontrol against eukaryotic plant pathogens, mycorrhization facilitation, and possibly resistance against protist predation. The diversity of T3SSs in plant-beneficial bacteria points to their important roles in multifarious interkingdom interactions in the rhizosphere. We argue that the gap in research on T3SSs in plant-beneficial bacteria must be bridged to better understand bacteria/eukaryotes rhizosphere interactions and to support the development of efficient plant-growth promoting microbial inoculants.

scholarly journals Tight Turns of Outer Membrane Proteins: An Analysis of Sequence, Structure, and Hydrogen Bonding

2018 ◽  
Author(s):  
Meghan Whitney Franklin ◽  
Joanna S.G. Slusky
Keyword(s):  
Hydrogen Bonding ◽  
Membrane Proteins ◽  
Outer Membrane ◽  
Soluble Protein ◽  
Structure Prediction ◽  
Outer Membrane Proteins ◽  
Sequence Structure ◽  
Structural Class ◽  
Future Design ◽  
Extracellular Loops

I.AbstractAs a structural class, tight turns can control molecular recognition, enzymatic activity, and nucleation of folding. They have been extensively characterized in soluble proteins but have not been characterized in outer membrane proteins (OMPs), where they also support critical functions. We clustered the 4-6 residue tight turns of 110 OMPs to characterize the phi/psi angles, sequence, and hydrogen bonding of these structures. We find significant differences between reports of soluble protein tight turns and OMP tight turns. Since OMP strands are less twisted than soluble strands they favor different turn structures types. Moreover, the membrane localization of OMPs yields different sequence hallmarks for their tight turns relative to soluble protein turns. We also characterize the differences in phi/psi angles, sequence, and hydrogen bonding between OMP extracellular loops and OMP periplasmic turns. As previously noted, the extracellular loops tend to be much longer than the periplasmic turns. We find that this difference in length is due to the broader distribution of lengths of the extracellular loops not a large difference in the median length. Extracellular loops also tend to have more charged residues as predicted by the charge-out rule. Finally, in all OMP tight turns, hydrogen bonding between the sidechain and backbone two to four residues away plays an important role. These bonds preferentially use an Asp, Asn, Ser or Thr residue in a beta or pro phi/psi conformation. We anticipate that this study will be applicable to future design and structure prediction of OMPs.

The entomopathogenic fungi Metarhizium brunneum and Beauveria bassiana promote systemic immunity and confer resistance to a broad range of pests and pathogens in tomato

2021 ◽  
Author(s):  
Rupali Gupta ◽  
Ravindran Keppanan ◽  
Meirav Leibman-Markus ◽  
Dalia Rav David ◽  
Yigal Elad ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Plant Growth ◽  
Beauveria Bassiana ◽  
Entomopathogenic Fungi ◽  
Plant Pathogens ◽  
Plant Immunity ◽  
Systemic Immunity ◽  
Metarhizium Brunneum ◽  
Promote Plant Growth ◽  
Arthropod Pests

Biocontrol agents can control pathogens by re-enforcing systemic plant resistance through systemic acquired resistance (SAR) or induced systemic resistance (ISR). Trichoderma spp. can activate the plant immune system through ISR, priming molecular mechanisms of defense against pathogens. Entomopathogenic fungi (EPF) can infect a wide range of arthropod pests, and play an important role in reducing pests' population. Here, we investigated the mechanisms by which EPF control plant diseases. We tested two well studied EPF, Metarhizium brunneum isolate Mb7 and Beauveria bassiana as the commercial product Velifer, for their ability to induce systemic immunity and disease resistance against several fungal and bacterial phytopathogens, and their ability to promote plant growth. We compared the activity of these EPF to an established biocontrol agent, T. harzianum T39, a known inducer of systemic plant immunity and broad disease resistance. The three fungal agents were effective against several fungal and bacterial plant pathogens and arthropod pests. Our results indicate that EPF induce systemic plant immunity and disease resistance by activating the plant host defense machinery, as evidenced by increases in reactive oxygen species (ROS) production and defense gene expression, and that EPF promote plant growth. EPF should be considered as control means for Tuta absoluta. We demonstrate that, with some exceptions, biocontrol in tomato can be equally potent by the tested EPF and T. harzianum T39, against both insect pests and plant pathogens. Taken together, our findings suggest that EPF may find use in broad-spectrum pest and disease management and as plant growth promoting agents.

scholarly journals Pseudomonas syringae AlgU Downregulates Flagellin Gene Expression, Helping Evade Plant Immunity

2019 ◽  
Vol 202 (4) ◽  
Author(s):  
Zhongmeng Bao ◽  
Hai-Lei Wei ◽  
Xing Ma ◽  
Bryan Swingle
Keyword(s):  
Gene Expression ◽  
Pseudomonas Syringae ◽  
Plant Pathogens ◽  
Control Point ◽  
Plant Colonization ◽  
Compensatory Mechanisms ◽  
Flagellin Gene ◽  
Content Type ◽  
Immune Systems ◽  
Plant Infection

ABSTRACT Flagella power bacterial movement through liquids and over surfaces to access or avoid certain environmental conditions, ultimately increasing a cell’s probability of survival and reproduction. In some cases, flagella and chemotaxis are key virulence factors enabling pathogens to gain entry and attach to suitable host tissues. However, flagella are not always beneficial; both plant and animal immune systems have evolved receptors to sense the proteins that make up flagellar filaments as signatures of bacterial infection. Microbes poorly adapted to avoid or counteract these immune functions are unlikely to be successful in host environments, and this selective pressure has driven the evolution of diverse and often redundant pathogen compensatory mechanisms. We tested the role of AlgU, the Pseudomonas extracytoplasmic function sigma factor σE/σ22 ortholog, in regulating flagellar expression in the context of Pseudomonas syringae-plant interactions. We found that AlgU is necessary for downregulating bacterial flagellin expression in planta and that this results in a corresponding reduction in plant immune elicitation. This AlgU-dependent regulation of flagellin gene expression is beneficial to bacterial growth in the course of plant infection, and eliminating the plant’s ability to detect flagellin makes this AlgU-dependent function irrelevant for bacteria growing in the apoplast. Together, these results add support to an emerging model in which P. syringae AlgU functions at a key control point that serves to optimize the expression of bacterial functions during host interactions, including minimizing the expression of immune elicitors and concomitantly upregulating beneficial virulence functions. IMPORTANCE Foliar plant pathogens, like Pseudomonas syringae, adjust their physiology and behavior to facilitate host colonization and disease, but the full extent of these adaptations is not known. Plant immune systems are triggered by bacterial molecules, such as the proteins that make up flagellar filaments. In this study, we found that during plant infection, AlgU, a gene expression regulator that is responsive to external stimuli, downregulates expression of fliC, which encodes the flagellin protein, a strong elicitor of plant immune systems. This change in gene expression and resultant change in behavior correlate with reduced plant immune activation and improved P. syringae plant colonization. The results of this study demonstrate the proximate and ultimate causes of flagellar regulation in a plant-pathogen interaction.

scholarly journals Indole-Containing Phytoalexin-Based Bioisosteres as Antifungals: In Vitro and In Silico Evaluation against Fusarium oxysporum

Molecules ◽  
2019 ◽  
Vol 25 (1) ◽  
pp. 45
Author(s):  
Andrea Angarita-Rodríguez ◽  
Diego Quiroga ◽  
Ericsson Coy-Barrera
Keyword(s):  
Fusarium Oxysporum ◽  
Mycelial Growth ◽  
Plant Pathogens ◽  
Antifungal Agents ◽  
Molecular Mechanic ◽  
Energy Performance ◽  
Fusarium Spp ◽  
Molecular Interaction Fields ◽  
Poisson Boltzmann

There is a continuous search for more reliable and effective alternatives to control phytopathogens through different strategies. In this context, indole-containing phytoalexins are stimuli-induced compounds implicated in plant defense against plant pathogens. However, phytoalexins’ efficacy have been limited by fungal detoxifying mechanisms, thus, the research on bioisosteres-based analogs can be a friendly alternative regarding the control of Fusarium phytopathogens, but there are currently few studies on it. Thus, as part of our research on antifungal agents, a set of 21 synthetic indole-containing phytoalexin analogs were evaluated as inhibitors against the phyopathogen Fusarium oxysporum. Results indicated that analogs of the N,N-dialkylthiourea, N,S-dialkyldithiocarbamate and substituted-1,3-thiazolidin-5-one groups exhibited the best docking scores and interaction profiles within the active site of Fusarium spp. enzymes. Vina scores exhibited correlation with experimental mycelial growth inhibition using supervised statistics, and this antifungal dataset correlated with molecular interaction fields after CoMFA. Compound 24 (tert-butyl (((3-oxo-1,3-diphenylpropyl)thio)carbonothioyl)-l-tryptophanate), a very active analog against F. oxysporum, exhibited the best interaction with lanosterol 14α-demethylase according to molecular docking, molecular dynamics and molecular mechanic/poisson-boltzmann surface area (MM/PBSA) binding energy performance. After data analyses, information on mycelial growth inhibitors, structural requirements and putative enzyme targets may be used in further antifungal development based on phytoalexin analogs for controlling phytopathogens.

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