What the transcriptome does not tell — proteomics and metabolomics are closer to the plants’ patho-phenotype

Feußner, Ivo; Polle, Andrea

doi:10.1016/j.pbi.2015.05.023

Cited by 120 publications

(83 citation statements)

References 68 publications

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“…However, the accumulation of steroidal saponins in this species has been reported only in rhizome1617, indicating their possible transport to rhizome, similar to ginsenosides biosynthesis in Panax spp56. As the rate of synthesis and the amount of accumulation of metabolites in different tissue are regulated by many factors such as, rate of transcription, translation, post- transcriptional and post-translational modifications, therefore, correlation cannot be established between biosynthesis and accumulation sites solely with the spatial transcriptome analysis57. Additionally, in perennial herbs, the synthesis and accumulation of specialized metabolites in different tissues is greatly influenced by the age and different developmental stages of the plant as reported in P. ginseng and P. quinquefolius , wherein older plants have higher content of ginsenosides in root, where as leaves accumulates higher metabolite content during early growth stages56.…”

Section: Discussionmentioning

confidence: 87%

Spatial transcriptome analysis provides insights of key gene(s) involved in steroidal saponin biosynthesis in medicinally important herb Trillium govanianum

Singh

Bhandawat

et al. 2017

Sci Rep

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Trillium govanianum, an endangered medicinal herb native to the Himalaya, is less studied at the molecular level due to the non-availability of genomic resources. To facilitate the basic understanding of the key genes and regulatory mechanism of pharmaceutically important biosynthesis pathways, first spatial transcriptome sequencing of T. govanianum was performed. 151,622,376 (~11.5 Gb) high quality reads obtained using paired-end Illumina sequencing were de novo assembled into 69,174 transcripts. Functional annotation with multiple public databases identified array of genes involved in steroidal saponin biosynthesis and other secondary metabolite pathways including brassinosteroid, carotenoid, diterpenoid, flavonoid, phenylpropanoid, steroid and terpenoid backbone biosynthesis, and important TF families (bHLH, MYB related, NAC, FAR1, bZIP, B3 and WRKY). Differentially expressed large number of transcripts, together with CYPs and UGTs suggests involvement of these candidates in tissue specific expression. Combined transcriptome and expression analysis revealed that leaf and fruit tissues are the main site of steroidal saponin biosynthesis. In conclusion, comprehensive genomic dataset created in the current study will serve as a resource for identification of potential candidates for genetic manipulation of targeted bioactive metabolites and also contribute for development of functionally relevant molecular marker resource to expedite molecular breeding and conservation efforts in T. govanianum.

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Section: Discussionmentioning

confidence: 87%

Spatial transcriptome analysis provides insights of key gene(s) involved in steroidal saponin biosynthesis in medicinally important herb Trillium govanianum

Singh

Bhandawat

et al. 2017

Sci Rep

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“…In order to elucidate gene function, the investigation of the gene product, the protein, is inevitable. The proteome does not only provide a complementary level to the transcriptome for studying the plethora of responses between plants and PGPB, proteins are also, together with metabolites, directly related to a phenotypical manifestation of a physiological response (Feussner and Polle, 2015). Enhancements in proteomic technology related to protein separation and detection as well as mass spectrometry-based protein identification have an increasing impact on the study of plant responses to biotic interactions (Mathesius, 2009; Cheng et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

A Proteomic Approach Suggests Unbalanced Proteasome Functioning Induced by the Growth-Promoting Bacterium Kosakonia radicincitans in Arabidopsis

et al. 2017

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Endophytic plant growth-promoting bacteria have significant impact on the plant physiology and understanding this interaction at the molecular level is of particular interest to support crop productivity and sustainable production systems. We used a proteomics approach to investigate the molecular mechanisms underlying plant growth promotion in the interaction of Kosakonia radicincitans DSM 16656 with Arabidopsis thaliana. Four weeks after the inoculation, the proteome of roots from inoculated and control plants was compared using two-dimensional gel electrophoresis and differentially abundant protein spots were identified by liquid chromatography tandem mass spectrometry. Twelve protein spots were responsive to the inoculation, with the majority of them being related to cellular stress reactions. The protein expression of 20S proteasome alpha-3 subunit was increased by the presence of K. radicincitans. Determination of proteasome activity and immuno blotting analysis for ubiquitinated proteins revealed that endophytic colonization interferes with ubiquitin-dependent protein degradation. Inoculation of rpn12a, defective in a 26S proteasome regulatory particle, enhanced the growth-promoting effect. This indicates that the plant proteasome, besides being a known target for plant pathogenic bacteria, is involved in the establishment of beneficial interactions of microorganisms with plants.

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“…Although, the protein abundances of the Gm NLLs could not be determined, all overexpression lines performed better than the wild type plants in the germination and root growth experiments. The differences between the lines could be explained by a combination of post-transcriptional, translational, and degradative regulation after the expression of mRNA (Vogel and Marcotte, 2012; Feussner and Polle, 2015). Future salt stress experiments on adult Arabidopsis plants could be helpful to investigate whether older plants also possess these salt tolerant characteristics and if GmNLL1 and GmNLL2 might be components of the regulatory pathways of salt stress in plants.…”

Section: Discussionmentioning

confidence: 99%

Overexpression of Nictaba-Like Lectin Genes from Glycine max Confers Tolerance toward Pseudomonas syringae Infection, Aphid Infestation and Salt Stress in Transgenic Arabidopsis Plants

2016

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Plants have evolved a sophisticated immune system that allows them to recognize invading pathogens by specialized receptors. Carbohydrate-binding proteins or lectins are part of this immune system and especially the lectins that reside in the nucleocytoplasmic compartment are known to be implicated in biotic and abiotic stress responses. The class of Nictaba-like lectins (NLL) groups all proteins with homology to the tobacco (Nicotiana tabacum) lectin, known as a stress-inducible lectin. Here we focus on two Nictaba homologs from soybean (Glycine max), referred to as GmNLL1 and GmNLL2. Confocal laser scanning microscopy of fusion constructs with the green fluorescent protein either transiently expressed in Nicotiana benthamiana leaves or stably transformed in tobacco BY-2 suspension cells revealed a nucleocytoplasmic localization for the GmNLLs under study. RT-qPCR analysis of the transcript levels for the Nictaba-like lectins in soybean demonstrated that the genes are expressed in several tissues throughout the development of the plant. Furthermore, it was shown that salt treatment, Phytophthora sojae infection and Aphis glycines infestation trigger the expression of particular NLL genes. Stress experiments with Arabidopsis lines overexpressing the NLLs from soybean yielded an enhanced tolerance of the plant toward bacterial infection (Pseudomonas syringae), insect infestation (Myzus persicae) and salinity. Our data showed a better performance of the transgenic lines compared to wild type plants, indicating that the NLLs from soybean are implicated in the stress response. These data can help to further elucidate the physiological importance of the Nictaba-like lectins from soybean, which can ultimately lead to the design of crop plants with a better tolerance to changing environmental conditions.

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What the transcriptome does not tell — proteomics and metabolomics are closer to the plants’ patho-phenotype

Cited by 120 publications

References 68 publications

Spatial transcriptome analysis provides insights of key gene(s) involved in steroidal saponin biosynthesis in medicinally important herb Trillium govanianum

Spatial transcriptome analysis provides insights of key gene(s) involved in steroidal saponin biosynthesis in medicinally important herb Trillium govanianum

A Proteomic Approach Suggests Unbalanced Proteasome Functioning Induced by the Growth-Promoting Bacterium Kosakonia radicincitans in Arabidopsis

Overexpression of Nictaba-Like Lectin Genes from Glycine max Confers Tolerance toward Pseudomonas syringae Infection, Aphid Infestation and Salt Stress in Transgenic Arabidopsis Plants

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