Insights into fruit function from the proteome of the hypanthium

Marondedze, Claudius; Thomas, Ludivine

doi:10.1016/j.jplph.2011.10.001

Cited by 7 publications

(4 citation statements)

References 62 publications

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“…Some protein spots were assigned to more than one protein, possibly because the proteins co-migrated as a result of having the same p I and molecular weight. This pattern of co-migration is not uncommon in proteomic studies and was reported previously [23,24]. The 31 up- and 22 down-regulated X .…”

Section: Resultssupporting

confidence: 80%

Insights into xanthomonas axonopodis pv. citri biofilm through proteomics

et al. 2013

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BackgroundXanthomonas axonopodis pv. citri (X. a. pv. citri) causes citrus canker that can result in defoliation and premature fruit drop with significant production losses worldwide. Biofilm formation is an important process in bacterial pathogens and several lines of evidence suggest that in X. a. pv. citri this process is a requirement to achieve maximal virulence since it has a major role in host interactions. In this study, proteomics was used to gain further insights into the functions of biofilms.ResultsIn order to identify differentially expressed proteins, a comparative proteomic study using 2D difference gel electrophoresis was carried out on X. a. pv. citri mature biofilm and planktonic cells. The biofilm proteome showed major variations in the composition of outer membrane proteins and receptor or transport proteins. Among them, several porins and TonB-dependent receptor were differentially regulated in the biofilm compared to the planktonic cells, indicating that these proteins may serve in maintaining specific membrane-associated functions including signaling and cellular homeostasis. In biofilms, UDP-glucose dehydrogenase with a major role in exopolysaccharide production and the non-fimbrial adhesin YapH involved in adherence were over-expressed, while a polynucleotide phosphorylase that was demonstrated to negatively control biofilm formation in E. coli was down-regulated. In addition, several proteins involved in protein synthesis, folding and stabilization were up-regulated in biofilms. Interestingly, some proteins related to energy production, such as ATP-synthase were down-regulated in biofilms. Moreover, a number of enzymes of the tricarboxylic acid cycle were differentially expressed. In addition, X. a. pv. citri biofilms also showed down-regulation of several antioxidant enzymes. The respective gene expression patterns of several identified proteins in both X. a. pv. citri mature biofilm and planktonic cells were evaluated by quantitative real-time PCR and shown to consistently correlate with those deduced from the proteomic study.ConclusionsDifferentially expressed proteins are enriched in functional categories. Firstly, proteins that are down-regulated in X. a. pv. citri biofilms are enriched for the gene ontology (GO) terms ‘generation of precursor metabolites and energy’ and secondly, the biofilm proteome mainly changes in ‘outer membrane and receptor or transport’. We argue that the differentially expressed proteins have a critical role in maintaining a functional external structure as well as enabling appropriate flow of nutrients and signals specific to the biofilm lifestyle.

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Section: Resultssupporting

confidence: 80%

Insights into xanthomonas axonopodis pv. citri biofilm through proteomics

et al. 2013

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“…The Delta 2D analysis revealed an average of 960 unique spots resolved on individual 2-DE and this is comparable to recently reported fruit proteome profiles. 27, 36–41 …”

Section: Resultsmentioning

confidence: 99%

Dynamic changes in the date palm fruit proteome during development and ripening

2014

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Date palm (Phoenix dactylifera) is an economically important fruit tree in the Middle East and North Africa and is characterized by large cultivar diversity, making it a good model for studies on fruit development and other important traits. Here in gel comparative proteomics combined with tandem mass spectrometry were used to study date fruit development and ripening. Total proteins were extracted using a phenol-based protocol. A total of 189 protein spots were differentially regulated (p≤0.05). The identified proteins were classified into 14 functional categories. The categories with the most proteins were ‘disease and defense’ (16.5%) and ‘metabolism’ (15.4%). Twenty-nine proteins have not previously been identified in other fleshy fruits and 64 showed contrasting expression patterns in other fruits. Abundance of most proteins with a role in abiotic stress responses increased during ripening with the exception of heat shock proteins. Proteins with a role in anthocyanin biosynthesis, glycolysis, tricarboxylic acid cycle and cell wall degradation were upregulated particularly from the onset of ripening and during ripening. In contrast, expression of pentose phosphate- and photosynthesis-related proteins decreased during fruit maturation. Although date palm is considered a climacteric species, the analysis revealed downregulation of two enzymes involved in ethylene biosynthesis, suggesting an ethylene-independent ripening of ‘Barhi’ fruits. In summary, this proteomics study provides insights into physiological processes during date fruit development and ripening at the systems level and offers a reference proteome for the study of regulatory mechanisms that can inform molecular and biotechnological approaches to further improvements of horticultural traits including fruit quality and yield.

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“…For proteomics analyses, standardized sample preparation that ensures consistent results is crucial in order to obtain high-quality resolution and greater coverage of the proteome [ 2 ] and allows the comparison of data from different studies. For example, proteins from apple ( Malus domestica ), avocado ( Persea americana ), banana ( Musa americana ) and orange ( Citrus × sinensis ) fruits extracted in a study using either a phenol/chloroform or a trichloroacetic acid (TCA) in acetone protocol yielded different proteome profiles [ 3 , 4 ]. Furthermore, plant proteomics presents difficulties caused by the structural characteristics of plant tissues including the cell wall matrix [ 3 , 5 , 6 , 7 , 8 ] and secondary metabolites that can cause problems in two-dimensional gel electrophoresis (2DE) and mass spectrometry (MS) [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

“…The latter two techniques also inhibit unwanted proteolytic activity of the sample during precipitation [ 17 ], while limiting interference with secondary metabolites [ 18 , 19 ]. Moreover, the combination of precipitation method and solubilization buffer can also cause differences in protein recovery and resulting proteomes [ 3 , 4 , 6 , 15 ]. Recent studies have started assessing the effects of detergent in solubilization on proteome coverage from E. coli [ 20 ] and biofilm-forming bacteria [ 21 ].…”

Section: Introductionmentioning

confidence: 99%

Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage

Marondedze

Wong

Groen

et al. 2014

IJMS

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The study of proteomes provides new insights into stimulus-specific responses of protein synthesis and turnover, and the role of post-translational modifications at the systems level. Due to the diverse chemical nature of proteins and shortcomings in the analytical techniques used in their study, only a partial display of the proteome is achieved in any study, and this holds particularly true for plant proteomes. Here we show that different solubilization and separation methods have profound effects on the resulting proteome. In particular, we observed that the type of detergents employed in the solubilization buffer preferentially enriches proteins in different functional categories. These include proteins with a role in signaling, transport, response to temperature stimuli and metabolism. This data may offer a functional bias on comparative analysis studies. In order to obtain a broader coverage, we propose a two-step solubilization protocol with first a detergent-free buffer and then a second step utilizing a combination of two detergents to solubilize proteins.

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Insights into fruit function from the proteome of the hypanthium

Cited by 7 publications

References 62 publications

Insights into xanthomonas axonopodis pv. citri biofilm through proteomics

Insights into xanthomonas axonopodis pv. citri biofilm through proteomics

Dynamic changes in the date palm fruit proteome during development and ripening

Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage

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