Secretome Profiling Reveals Virulence-Associated Proteins of Fusarium proliferatum during Interaction with Banana Fruit

Secreted proteins are vital for the pathogenicity of many fungi through manipulating their hosts for efficient colonization. Fusarium proliferatum is a phytopathogenic fungus infecting many crops, vegetables, and fruit, including banana fruit. To access the proteins involved in pathogen–host interaction, we used label-free quantitative proteomics technology to comparatively analyze the secretomes of F. proliferatum cultured with and without banana peel in Czapek’s broth medium. By analyzing the secretomes of F. proliferatum, we have identified 105 proteins with 40 exclusively secreted and 65 increased in abundance in response to a banana peel. These proteins were involved in the promotion of invasion of banana fruit, and they were mainly categorized into virulence factors, cell wall degradation, metabolic process, response to stress, regulation, and another unknown biological process. The expressions of corresponding genes confirmed the existence of these secreted proteins in the banana peel. Furthermore, expression pattern suggested variable roles for these genes at different infection stages. This study expanded the current database of F. proliferatum secreted proteins which might be involved in the infection strategy of this fungus. Additionally, this study warranted the further attention of some secreted proteins that might initiate infection of F. proliferatum on banana fruit.

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Effects of Different Carbon Sources on Fumonisin Production and FUM Gene Expression by Fusarium proliferatum

Toxins ◽

10.3390/toxins11050289 ◽

2019 ◽

Vol 11 (5) ◽

pp. 289 ◽

Cited By ~ 2

Author(s):

Yu Wu ◽

Taotao Li ◽

Liang Gong ◽

Yong Wang ◽

Yueming Jiang

Keyword(s):

Carbon Source ◽

Biological Effect ◽

Culture Medium ◽

Carbon Sources ◽

Fusarium Proliferatum ◽

Banana Peel ◽

Transcriptional Level ◽

Banana Fruit ◽

Limited Information ◽

Future Work

Fusarium proliferatum can infect many crops and then produce fumonisins that are very harmful to humans and animals. Previous study indicates that carbon sources play important roles in regulating the fumonisin biosynthesis. Unfortunately, there is limited information on the effects of carbon starvation in comparison with the carbon sources present in the host of fumonisin production in F. proliferatum. Our results indicated that F. proliferatum cultivated in the Czapek’s broth (CB) medium in the absence of sucrose could greatly induce production of fumonisin, while an additional supplementation of sucrose to the culture medium significantly reduced the fumonisin production. Furthermore, cellulose and hemicellulose, and polysaccharide extracted from banana peel, which replaced sucrose as the carbon source, can reduce the production of fumonisin by F. proliferatum. Further work showed that these genes related to the synthesis of fumonisin, such as FUM1 and FUM8, were significantly up-regulated in the culture medium in the absence of sucrose. Consistent with fumonisin production, the expressions of FUM gene cluster and ZFR1 gene decreased after the addition of sucrose. Moreover, these genes were also significantly down-regulated in the presence of cellulose, hemicellulose or polysaccharide extracted from peel. Altogether, our results suggested that fumonisin production was regulated in F. proliferatum in response to different carbon source conditions, and this regulation might be mainly via the transcriptional level. Future work on these expressions of the fumonisin biosynthesis-related genes is needed to further clarify the response under different carbon conditions during the infection of F. proliferatum on banana fruit hosts. The findings in this study will provide a new clue regarding the biological effect of the fumonisin production in response to environmental stress.

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Structural Analysis of Jumbo Coliphage phAPEC6

International Journal of Molecular Sciences ◽

10.3390/ijms21093119 ◽

2020 ◽

Vol 21 (9) ◽

pp. 3119 ◽

Cited By ~ 3

Author(s):

Jeroen Wagemans ◽

Jessica Tsonos ◽

Dominique Holtappels ◽

Kiandro Fortuna ◽

Jean-Pierre Hernalsteens ◽

...

Keyword(s):

Electron Microscopy ◽

Capsid Protein ◽

Tem Analysis ◽

Host Interaction ◽

Cryo Electron Microscopy ◽

Transmission Electron ◽

Tail Sheath ◽

Associated Proteins ◽

Contractile Tail ◽

Phage Capsid

The phAPEC6 genome encodes 551 predicted gene products, with the vast majority (83%) of unknown function. Of these, 62 have been identified as virion-associated proteins by mass spectrometry (ESI-MS/MS), including the major capsid protein (Gp225; present in 1620 copies), which shows a HK97 capsid protein-based fold. Cryo-electron microscopy experiments showed that the 350-kbp DNA molecule of Escherichia coli virus phAPEC6 is packaged in at least 15 concentric layers in the phage capsid. A capsid inner body rod is also present, measuring about 91 nm by 18 nm and oriented along the portal axis. In the phAPEC6 contractile tail, 25 hexameric stacked rings can be distinguished, built of the identified tail sheath protein (Gp277). Cryo-EM reconstruction reveals the base of the unique hairy fibers observed during an initial transmission electron microscopy (TEM) analysis. These very unusual filaments are ordered at three annular positions along the contractile sheath, as well as around the capsid, and may be involved in host interaction.

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Fumonisin B1 induced aggressiveness and infection mechanism of Fusarium proliferatum on banana fruit

Environmental Pollution ◽

10.1016/j.envpol.2021.117793 ◽

2021 ◽

pp. 117793

Author(s):

Lihong Xie ◽

Yanfei Wu ◽

Yong Wang ◽

Yueming Jiang ◽

Bao Yang ◽

...

Keyword(s):

Fumonisin B1 ◽

Fusarium Proliferatum ◽

Banana Fruit ◽

Infection Mechanism

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A Comparative Quantitative LC-MS/MS Profiling Analysis of Human Pancreatic Adenocarcinoma, Adjacent-Normal Tissue, and Patient-Derived Tumour Xenografts

Proteomes ◽

10.3390/proteomes6040045 ◽

2018 ◽

Vol 6 (4) ◽

pp. 45 ◽

Cited By ~ 12

Author(s):

Orla Coleman ◽

Michael Henry ◽

Fiona O'Neill ◽

Sandra Roche ◽

Niall Swan ◽

...

Keyword(s):

Proteomic Analysis ◽

Normal Tissue ◽

Rapid Development ◽

Ductal Adenocarcinoma ◽

Adjacent Normal Tissue ◽

Label Free ◽

Normal Pancreas ◽

Human Tumour Cells ◽

Associated Proteins ◽

Pdx Models

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers worldwide; it develops in a relatively symptom-free manner, leading to rapid disease progression and metastasis, leading to a 5-year survival rate of less than 5%. A lack of dependable diagnostic markers and rapid development of resistance to conventional therapies are among the problems associated with management of the disease. A better understanding of pancreatic tumour biology and discovery of new potential therapeutic targets are important goals in pancreatic cancer research. This study describes the comparative quantitative LC-MS/MS proteomic analysis of the membrane-enriched proteome of 10 human pancreatic ductal adenocarcinomas, 9 matched adjacent-normal pancreas and patient-derived xenografts (PDXs) in mice (10 at F1 generation and 10 F2). Quantitative label-free LC-MS/MS data analysis identified 129 proteins upregulated, and 109 downregulated, in PDAC, compared to adjacent-normal tissue. In this study, analysing peptide MS/MS data from the xenografts, great care was taken to distinguish species-specific peptides definitively derived from human sequences, or from mice, which could not be distinguished. The human-only peptides from the PDXs are of particular value, since only human tumour cells survive, and stromal cells are replaced during engraftment in the mouse; this list is, therefore, enriched in tumour-associated proteins, some of which might be potential therapeutic or diagnostic targets. Using human-specific sequences, 32 proteins were found to be upregulated, and 113 downregulated in PDX F1 tumours, compared to primary PDAC. Differential expression of CD55 between PDAC and normal pancreas, and expression across PDX generations, was confirmed by Western blotting. These data indicate the value of using PDX models in PDAC research. This study is the first comparative proteomic analysis of PDAC which employs PDX models to identify patient tumour cell-associated proteins, in an effort to find robust targets for therapeutic treatment of PDAC.

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Proteomic and physiological analysis provides an elucidation of Fusarium proliferatum infection causing crown rot on banana fruit

Microbiological Research ◽

10.1016/j.micres.2021.126952 ◽

2021 ◽

pp. 126952

Author(s):

Lihong Xie ◽

Yanfei Wu ◽

Xuewu Duan ◽

Taotao Li ◽

Yueming Jiang

Keyword(s):

Fusarium Proliferatum ◽

Crown Rot ◽

Banana Fruit ◽

Physiological Analysis

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Oligomeric amyloid-β induces early and widespread changes to the proteome in human iPSC-derived neurons

Scientific Reports ◽

10.1038/s41598-020-63398-6 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 2

Author(s):

Christopher Sackmann ◽

Martin Hallbeck

Keyword(s):

Amyloid Β ◽

Brain Regions ◽

Tau Proteins ◽

Label Free ◽

Human Neurons ◽

Associated Proteins ◽

Proteasome Subunits ◽

Heterogeneous Nuclear Ribonucleoproteins ◽

Human Ipsc ◽

Differential Phosphorylation

AbstractAlzheimer’s disease (AD) is the most common form of dementia globally and is characterized by aberrant accumulations of amyloid-beta (Aβ) and tau proteins. Oligomeric forms of these proteins are believed to be most relevant to disease progression, with oligomeric amyloid-β (oAβ) particularly implicated in AD. oAβ pathology spreads among interconnected brain regions, but how oAβ induces pathology in these previously unaffected neurons requires further study. Here, we use well characterized iPSC-derived human neurons to study the early changes to the proteome and phosphoproteome after 24 h exposure to oAβ 1-42. Using nLC-MS/MS and label-free quantification, we identified several proteins that are differentially regulated in response to acute oAβ challenge. At this early timepoint, oAβ induced the decrease of TDP-43, heterogeneous nuclear ribonucleoproteins (hnRNPs), and coatomer complex I (COPI) proteins. Conversely, increases were observed in 20 S proteasome subunits and vesicle associated proteins VAMP1/2, as well as the differential phosphorylation of tau at serine 208. These changes show that there are widespread alterations to the neuronal proteome within 24 h of oAβ uptake, including proteins previously not shown to be related to neurodegeneration. This study provides new targets for the further study of early mediators of AD pathogenesis.

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Comparison of the Genome Sequence of the Poultry Pathogen Bordetella avium with Those of B. bronchiseptica, B. pertussis, and B. parapertussis Reveals Extensive Diversity in Surface Structures Associated with Host Interaction

Journal of Bacteriology ◽

10.1128/jb.01927-05 ◽

2006 ◽

Vol 188 (16) ◽

pp. 6002-6015 ◽

Cited By ~ 54

Author(s):

Mohammed Sebaihia ◽

Andrew Preston ◽

Duncan J. Maskell ◽

Holly Kuzmiak ◽

Terry D. Connell ◽

...

Keyword(s):

Genome Sequence ◽

Outer Membrane Proteins ◽

Phase Variation ◽

Regulatory System ◽

Secreted Proteins ◽

Type I ◽

Host Interaction ◽

Bordetella Avium ◽

Evolutionary Relatedness ◽

Large Genes

ABSTRACT Bordetella avium is a pathogen of poultry and is phylogenetically distinct from Bordetella bronchiseptica, Bordetella pertussis, and Bordetella parapertussis, which are other species in the Bordetella genus that infect mammals. In order to understand the evolutionary relatedness of Bordetella species and further the understanding of pathogenesis, we obtained the complete genome sequence of B. avium strain 197N, a pathogenic strain that has been extensively studied. With 3,732,255 base pairs of DNA and 3,417 predicted coding sequences, it has the smallest genome and gene complement of the sequenced bordetellae. In this study, the presence or absence of previously reported virulence factors from B. avium was confirmed, and the genetic bases for growth characteristics were elucidated. Over 1,100 genes present in B. avium but not in B. bronchiseptica were identified, and most were predicted to encode surface or secreted proteins that are likely to define an organism adapted to the avian rather than the mammalian respiratory tracts. These include genes coding for the synthesis of a polysaccharide capsule, hemagglutinins, a type I secretion system adjacent to two very large genes for secreted proteins, and unique genes for both lipopolysaccharide and fimbrial biogenesis. Three apparently complete prophages are also present. The BvgAS virulence regulatory system appears to have polymorphisms at a poly(C) tract that is involved in phase variation in other bordetellae. A number of putative iron-regulated outer membrane proteins were predicted from the sequence, and this regulation was confirmed experimentally for five of these.

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Network Analysis of a Membrane-Enriched Brain Proteome across Stages of Alzheimer’s Disease

Proteomes ◽

10.3390/proteomes7030030 ◽

2019 ◽

Vol 7 (3) ◽

pp. 30 ◽

Cited By ~ 2

Author(s):

Lenora Higginbotham ◽

Eric Dammer ◽

Duc Duong ◽

Erica Modeste ◽

Thomas Montine ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Network Analysis ◽

Proteomic Analysis ◽

Expression Patterns ◽

Label Free ◽

Post Mortem Brain ◽

Brain Proteome ◽

Associated Proteins ◽

Membrane Bound

Previous systems-based proteomic approaches have characterized alterations in protein co-expression networks of unfractionated asymptomatic (AsymAD) and symptomatic Alzheimer’s disease (AD) brains. However, it remains unclear how sample fractionation and sub-proteomic analysis influences the organization of these protein networks and their relationship to clinicopathological traits of disease. In this proof-of-concept study, we performed a systems-based sub-proteomic analysis of membrane-enriched post-mortem brain samples from pathology-free control, AsymAD, and AD brains (n = 6 per group). Label-free mass spectrometry based on peptide ion intensity was used to quantify the 18 membrane-enriched fractions. Differential expression and weighted protein co-expression network analysis (WPCNA) were then used to identify and characterize modules of co-expressed proteins most significantly altered between the groups. We identified a total of 27 modules of co-expressed membrane-associated proteins. In contrast to the unfractionated proteome, these networks did not map strongly to cell-type specific markers. Instead, these modules were principally organized by their associations with a wide variety of membrane-bound compartments and organelles. Of these, the mitochondrion was associated with the greatest number of modules, followed by modules linked to the cell surface compartment. In addition, we resolved networks with strong associations to the endoplasmic reticulum, Golgi apparatus, and other membrane-bound organelles. A total of 14 of the 27 modules demonstrated significant correlations with clinical and pathological AD phenotypes. These results revealed that the proteins within individual compartments feature a heterogeneous array of AD-associated expression patterns, particularly during the preclinical stages of disease. In conclusion, this systems-based analysis of the membrane-associated AsymAD brain proteome yielded a unique network organization highly linked to cellular compartmentalization. Further study of this membrane-associated proteome may reveal novel insight into the complex pathways governing the earliest stages of disease.

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Label-Free Comparative Proteomic Analysis Combined with Laser-Capture Microdissection Suggests Important Roles of Stress Responses in the Black Layer of Maize Kernels

International Journal of Molecular Sciences ◽

10.3390/ijms21041369 ◽

2020 ◽

Vol 21 (4) ◽

pp. 1369

Author(s):

Quanquan Chen ◽

Ran Huang ◽

Zhenxiang Xu ◽

Yaxin Zhang ◽

Li Li ◽

...

Keyword(s):

Laser Capture Microdissection ◽

Stress Responses ◽

Label Free ◽

Kernel Development ◽

Flight Mass Spectrometry ◽

Specific Proteins ◽

Response To Stress ◽

Black Layer ◽

Maize Kernels ◽

Laser Capture

The black layer (BL) is traditionally used as an indicator for kernel harvesting in maize, as it turns visibly dark when the kernel reaches physiological maturity. However, the molecular roles of BL in kernel development have not been fully elucidated. In this work, microscopy images showed that BL began to appear at a growth stage earlier than 10 days after pollination (DAP), and its color gradually deepened to become dark as the development period progressed. Scanning electron microscopy observations revealed that BL is a tissue structure composed of several layers of cells that are gradually squeezed and compressed during kernel development. Laser-capture microdissection (LCM) was used to sample BL and its neighboring inner tissue, basal endosperm transfer layer (BETL), and outer tissue, inner epidermis (IEP), from 20 DAP of kernels. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry profiling (MALDI-TOF MS profiling) detected 41, 104, and 120 proteins from LCM-sampled BL, BETL, and IEP, respectively. Gene ontology (GO) analysis indicated that the 41 BL proteins were primarily involved in the response to stress and stimuli. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis found that the BL proteins were enriched in several defense pathways, such as the ascorbate and aldarate metabolic pathways. Among the 41 BL proteins, six were BL-specific proteins that were only detected from BL. Annotations of five BL-specific proteins were related to stress responses. During kernel development, transcriptional expression of most BL proteins showed an increase, followed by a decrease, and reached a maximum zero to 20 DAP. These results suggest a role for BL in stress responses for protecting filial tissue against threats from maternal sides, which helps to elucidate the biological functions of BL.

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