The membrane proteome of male gametophyte in Solanum lycopersicum

Paul, Puneet; Chaturvedi, Palak; Selymesi, Mario; Ghatak, Arindam; Mesihovic, Anida; Scharf, Klaus‐Dieter; Weckwerth, Wolfram; Simm, Stefan; Schleiff, Enrico

doi:10.1016/j.jprot.2015.10.009

Cited by 25 publications

(18 citation statements)

References 110 publications

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“…After sequencing, all libraries were aligned to the tomato genome of cultivar Heinz with the spliced aligner TopHat2 37 . In contrast to de novo or reference based transcriptome assembly, 35 the alignment to a reference genome allows the expression analysis and the detection of AS events for annotated genes. A high Pearson correlation between the read counts of biological replicates (Supplementary Materials S4), allowed us to merge their alignments into a single file leading to four samples to be analysed (Moneymaker CO, Moneymaker HS, Red Setter CO and Red Setter HS) with a total amount of more than 280 million reads each (Table 1).…”

Section: Resultsmentioning

confidence: 99%

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Alternative splicing in tomato pollen in response to heat stress

Keller¹,

Hu²,

Mesihovic³

et al. 2016

DNA Res

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Alternative splicing (AS) is a key control mechanism influencing signal response cascades in different developmental stages and under stress conditions. In this study, we examined heat stress (HS)-induced AS in the heat sensitive pollen tissue of two tomato cultivars. To obtain the entire spectrum of HS-related AS, samples taken directly after HS and after recovery were combined and analysed by RNA-seq. For nearly 9,200 genes per cultivar, we observed at least one AS event under HS. In comparison to control, for one cultivar we observed 76% more genes with intron retention (IR) or exon skipping (ES) under HS. Furthermore, 2,343 genes had at least one transcript with IR or ES accumulated under HS in both cultivars. These genes are involved in biological processes like protein folding, gene expression and heat response. Transcriptome assembly of these genes revealed that most of the alternative spliced transcripts possess truncated coding sequences resulting in partial or total loss of functional domains. Moreover, 141 HS specific and 22 HS repressed transcripts were identified. Further on, we propose AS as layer of stress response regulating constitutively expressed genes under HS by isoform abundance.

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Section: Resultsmentioning

confidence: 99%

“…Plant RNA Kit (Omega Bio-Tek, Norcross, GA, USA). Total RNA was used for the preparation of mRNA-seq libraries (GenXPro GmbH, Frankfurt Main, Germany) by performing rRNA depletion and enrichment of mRNA via polyadenylation (polyA) selection and purification 35 . Constructed libraries from each replicate of cv.…”

Section: Methodsmentioning

confidence: 99%

Alternative splicing in tomato pollen in response to heat stress

Keller¹,

Hu²,

Mesihovic³

et al. 2016

DNA Res

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“…GO classification of identified and protein localisation prediction were performed as previously described (Paul et al . ). Results are given in Table S2.…”

Section: Methodsmentioning

confidence: 97%

The outer membrane Omp85‐like protein P39 influences metabolic homeostasis in mature Arabidopsis thaliana

et al. 2018

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The Omp85 proteins form a large membrane protein family in bacteria and eukaryotes. Omp85 proteins are composed of a C-terminal β-barrel-shaped membrane domain and one or more N-terminal polypeptide transport-associated (POTRA) domains. However, Arabidopsis thaliana contains two genes coding for Omp85 proteins without a POTRA domain. One gene is designated P39, according to the molecular weight of the encoded protein. The protein is targeted to plastids and it was established that p39 has electrophysiological properties similar to other Omp85 family members, particularly to that designated as Toc75V/Oep80. We analysed expression of the gene and characterised two T-DNA insertion mutants, focusing on alterations in photosynthetic activity, plastid ultrastructure, global expression profile and metabolome. We observed pronounced expression of P39, especially in veins. Mutants of P39 show growth aberrations, reduced photosynthetic activity and changes in plastid ultrastructure, particularly in the leaf tip. Further, they display global alteration of gene expression and metabolite content in leaves of mature plants. We conclude that the function of the plastid-localised and vein-specific Omp85 family protein p39 is important, but not essential, for maintenance of metabolic homeostasis of full-grown A. thaliana plants. Further, the function of p39 in veins influences the functionality of other plant tissues. The link connecting p39 function with metabolic regulation in mature A. thaliana is discussed.

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“…Proteomic analyses had been conducted in the identification of anther and pollen proteins in normal microspore development, changes in anther proteins due to abiotic stress, and male‐sterility (Figure , Table ). In recent years, many cell‐specific and subcellular anther proteomic studies emerged, which facilitate understanding the role and function of a specific protein in a specific cell type and subcellular organ (Table ). For example, two studies performed by Chaturvedi et al.…”

Section: Introductionmentioning

confidence: 99%

Proteomes and Phosphoproteomes of Anther and Pollen: Availability and Progress

Zhang

Feng

et al. 2017

Proteomics

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In flowering plants, anther development plays crucial role in sexual reproduction. Within the anther, microspore mother cells meiosis produces microspores, which further develop into pollen grains that play decisive role in plant reproduction. Previous studies on anther biology mainly focused on single gene functions relying on genetic and molecular methods. Recently, anther development has been expanded from multiple OMICS approaches like transcriptomics, proteomics/phosphoproteomics, and metabolomics. The development of proteomics techniques allowing increased proteome coverage and quantitative measurements of proteins which can characterize proteomes and their modulation during normal development, biotic and abiotic stresses in anther development. In this review, we summarize the achievements of proteomics and phosphoproteomics with anther and pollen organs from model plant and crop species (i.e. Arabidopsis, rice, tobacco). The increased proteomic information facilitated translation of information from the models to crops and thus aid in agricultural improvement.

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The membrane proteome of male gametophyte in Solanum lycopersicum

Cited by 25 publications

References 110 publications

Alternative splicing in tomato pollen in response to heat stress

Alternative splicing in tomato pollen in response to heat stress

The outer membrane Omp85‐like protein P39 influences metabolic homeostasis in mature Arabidopsis thaliana

Proteomes and Phosphoproteomes of Anther and Pollen: Availability and Progress

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