iTRAQ-based proteomic analyses of the plant-pathogenic bacterium Acidovorax citrulli during entrance into and resuscitation from the viable but nonculturable state

Kan, Yumin; Lyu, Qingyang; Jiang, Na; Han, Song; Li, Jianqiang; Burdman, Saul; Luo, Laixin

doi:10.1016/j.jprot.2019.103547

Cited by 13 publications

(8 citation statements)

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“…Frozen bacterial samples stored in −80°C were transferred to shaking tubes, and lysis buffer was added to the samples and mixed well (Kan et al, 2020). A high-throughput tissue grinder was used and shaken three times for 40 s each time.…”

Section: Polypeptide Preparationmentioning

confidence: 99%

Effects of Simulated Microgravity on the Physiology of Stenotrophomonas maltophilia and Multiomic Analysis

Guo

Fang

et al. 2021

Front. Microbiol.

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Many studies have shown that the space environment plays a pivotal role in changing the characteristics of conditional pathogens, especially their pathogenicity and virulence. However, Stenotrophomonas maltophilia, a type of conditional pathogen that has shown to a gradual increase in clinical morbidity in recent years, has rarely been reported for its impact in space. In this study, S. maltophilia was exposed to a simulated microgravity (SMG) environment in high-aspect ratio rotating-wall vessel bioreactors for 14days, while the control group was exposed to the same bioreactors in a normal gravity (NG) environment. Then, combined phenotypic, genomic, transcriptomic, and proteomic analyses were conducted to compare the influence of the SMG and NG on S. maltophilia. The results showed that S. maltophilia in simulated microgravity displayed an increased growth rate, enhanced biofilm formation ability, increased swimming motility, and metabolic alterations compared with those of S. maltophilia in normal gravity and the original strain of S. maltophilia. Clusters of Orthologous Groups (COG) annotation analysis indicated that the increased growth rate might be related to the upregulation of differentially expressed genes (DEGs) involved in energy metabolism and conversion, secondary metabolite biosynthesis, transport and catabolism, intracellular trafficking, secretion, and vesicular transport. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that the increased motility might be associated the upregulation of differentially expressed proteins (DEPs) involved in locomotion, localization, biological adhesion, and binding, in accordance with the upregulated DEGs in cell motility according to COG classification, including pilP, pilM, flgE, flgG, and ronN. Additionally, the increased biofilm formation ability might be associated with the upregulation of DEPs involved in biofilm formation, the bacterial secretion system, biological adhesion, and cell adhesion, which were shown to be regulated by the differentially expressed genes (chpB, chpC, rpoN, pilA, pilG, pilH, and pilJ) through the integration of transcriptomic and proteomic analyses. These results suggested that simulated microgravity might increase the level of corresponding functional proteins by upregulating related genes to alter physiological characteristics and modulate growth rate, motility, biofilm formation, and metabolism. In conclusion, this study is the first general analysis of the phenotypic, genomic, transcriptomic, and proteomic changes in S. maltophilia under simulated microgravity and provides some suggestions for future studies of space microbiology.

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Section: Polypeptide Preparationmentioning

confidence: 99%

Effects of Simulated Microgravity on the Physiology of Stenotrophomonas maltophilia and Multiomic Analysis

Guo

Fang

et al. 2021

Front. Microbiol.

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“…For example, over a hundred pathogenicity and virulence-related factors of the nonoomycete Fusarium graminearum were discovered with the use of NGS and proteomics [48]. Another efficient and accurate tool is iTRAQ (isobaric tags for relative and absolute quantification) [49,50] for the analysis of protein profiles and signaling pathways. In N. benthamiana, this approach led to the identification of 2964 proteins in plants treated with the elicitin INF-1, two of which were shown to be essential in INF-1-triggered cell death responses.…”

Section: Proteomic Approachesmentioning

confidence: 99%

How to Unravel the Key Functions of Cryptic Oomycete Elicitin Proteins and Their Role in Plant Disease

Kharel

Islam

Rookes

et al. 2021

Plants

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Pathogens and plants are in a constant battle with one another, the result of which is either the restriction of pathogen growth via constitutive or induced plant defense responses or the pathogen colonization of plant cells and tissues that cause disease. Elicitins are a group of highly conserved proteins produced by certain oomycete species, and their sterol binding ability is recognized as an important feature in sterol–auxotrophic oomycetes. Elicitins also orchestrate other aspects of the interactions of oomycetes with their plant hosts. The function of elicitins as avirulence or virulence factors is controversial and is dependent on the host species, and despite several decades of research, the function of these proteins remains elusive. We summarize here our current understanding of elicitins as either defense-promoting or defense-suppressing agents and propose that more recent approaches such as the use of ‘omics’ and gene editing can be used to unravel the role of elicitins in host–pathogen interactions. A better understanding of the role of elicitins is required and deciphering their role in host–pathogen interactions will expand the strategies that can be adopted to improve disease resistance and reduce crop losses.

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“…ropB and gyrB were also used as the reference genes in some species, such as Burkholderia pyrrocinia, Herbaspirillum seropedicae and Hymenobacter daejeonensis (Jin et al, 2018;Pessoa et al, 2016;Wu et al, 2017). recA (DNA recombination and repair) and ugpB (snglycerol-3-phosphate ABC transporter ATP-binding protein) were selected as the reference genes in A. citrulli (Kan et al, 2020). To our knowledge, screening of suitable internal genes for specific biological processes analysis has not been reported in X. campestris pv.…”

Section: Various Methods For Gene Expression Detection Have Been Usedmentioning

confidence: 99%

“…recA (DNA recombination and repair) and ugpB (sn‐glycerol‐3‐phosphate ABC transporter ATP‐binding protein) were selected as the reference genes in A . citrulli (Kan et al, 2020). To our knowledge, screening of suitable internal genes for specific biological processes analysis has not been reported in X .…”

Section: Introductionmentioning

confidence: 99%

Evaluation of optimal reference genes for the normalization by qPCR in viable but nonculturable state in Xanthomonas campestris pv. campestris

Bai

Chen

Kan

et al. 2022

Journal of Phytopathology

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Xanthomonas campestris pv. campestris (Xcc), the pathogen of black rot of crucifers, could be induced into the viable but nonculturable (VBNC) state under stress, such as being induced by low concentration of Cu 2+ and acid condition induction. The main objective of current study was to select the optimal reference genes for data normalization by qPCR in the VBNC state of Xcc. In this study, Xcc was induced into VBNC state by Cu 2+ with an initial concentration of OD 600 = 0.18 and OD 600 = 0.45, and all viable bacterial cells lost the culturability and entered into the VBNC state at 24 h and 48 h respectively. The concentration of VBNC cells was 3.3 × 10 7 cells/ ml and 1.5 × 10 7 cells/ml respectively. Eight candidate reference genes (gyrB, pbpA, gapA, rpoB, tufA, 16S rRNA, ugpC and recA) were selected to assess the expression stability in the VBNC state of Xcc by four algorithms (geNorm, NormFinder, delta-Ct and BestKeeper), while RefFinder was used to integrate the output from the four algorithms in fine. According to the algorithm analysis and validation of clpX expression analysis, the most suitable reference gene this study identified was the combination of ugpC and pbpA, and the least suitable gene was 16S rRNA in the Xcc VBNC state. In this study, we identified the most stable internal controls under Cu 2+ -inducing conditions for calibration qRT-PCR analyses of Xanthomonas campestris pv. campestris and will be helpful to explore the stress resistance mechanism in this bacterium.

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iTRAQ-based proteomic analyses of the plant-pathogenic bacterium Acidovorax citrulli during entrance into and resuscitation from the viable but nonculturable state

Cited by 13 publications

References 50 publications

Effects of Simulated Microgravity on the Physiology of Stenotrophomonas maltophilia and Multiomic Analysis

Effects of Simulated Microgravity on the Physiology of Stenotrophomonas maltophilia and Multiomic Analysis

How to Unravel the Key Functions of Cryptic Oomycete Elicitin Proteins and Their Role in Plant Disease

Evaluation of optimal reference genes for the normalization by qPCR in viable but nonculturable state in Xanthomonas campestris pv. campestris

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