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ISSN: 2329-8936
Transcriptomics: Open Access
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Transcriptome and Proteome Profiling for Analyzing Fates of Global Gene Expression in Plant-Beneficial Bacilli

Rainer Borriss*
Section Phytomedicine, Albrecht Daniel Thaer - Institute of Agricultural and Horticultural Sciences, Faculty of Life Sciences, Humboldt University, Berlin, Lentzeallee 55- 57, 14195, Berlin, Germany
Corresponding Author : Rainer Borriss
Section Phytomedicine
Albrecht Daniel
Thaer - Institute of Agricultural and Horticultural Sciences
Faculty of Life Sciences, Humboldt University
Berlin , Lentzeallee 55-57, 14195 Berlin, Germany
Tel: +49 30 2093 46444
E-mail: [email protected]
Received: May 05, 2015 Accepted: May 16, 2015 Published: May 19, 2015
Citation: Borriss R (2015) Transcriptome and Proteome Profiling for Analyzing Fates of Global Gene Expression in Plant-Beneficial Bacilli. Transcriptomics 3: e110. doi:10.4172/2329-8936.1000e110
Copyright: ©2015 Borriss R. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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Abstract

Bacteria that are associated with plant roots and exert beneficial effects on plant development are referred to as plant-growth-promoting rhizobacteria (PGPR) [1]. In many cases, their plant-growth-promoting activity is linked with their ability to suppress soil-borne plant pathogens. Besides production of antimicrobial and nematocidal compounds, also stimulation of plant-induced systemic resistance (ISR) and subtle pathogen-biocontrol interactions contribute to their suppressive effects [2]. In course of the last twenty years or so, PGPR have been successfully applied to a wide range of agricultural species to enhance their yield and to avoid harvest damages caused by plant pathogens in a environmentally friendly way.

 
Bacteria that are associated with plant roots and exert beneficial effects on plant development are referred to as plant-growth-promoting rhizobacteria (PGPR) [1]. In many cases, their plant-growth-promoting activity is linked with their ability to suppress soil-borne plant pathogens. Besides production of antimicrobial and nematocidal compounds, also stimulation of plant-induced systemic resistance (ISR) and subtle pathogen-biocontrol interactions contribute to their suppressive effects [2]. In course of the last twenty years or so, PGPR have been successfully applied to a wide range of agricultural species to enhance their yield and to avoid harvest damages caused by plant pathogens in a environmentally friendly way. Plant-associated Bacilli are preferred in this context due to their ability to produce heat-resistant and durable endospores ensuring a long shelf life of the respective bioformulation [3]. In order to improve the beneficial action of those bioformulations on plant development it is highly important to understand the interactions of the applied bacterium and their host plant on the molecular level. In recent years, transcriptome-and proteome-analysis have been proven as efficient in enlarging our knowledge base in this topic. The first global study about gene expression in Bacillus using DNA-microarrays and 2-D protein gel electrophoresis was performed in 2001 using the laboratory model strain B. subtilis 168 [4]. The same model bacterium was used to analyze the global gene response against salicylic acid, an important plant signal compound. Proteome and transcriptome analysis indicated that protein destruction due to salicylic acid led to induction of detoxifying phenolic acid decarboxylases [5]. A DNA microarray supported transcriptome analysis of B. subtilis OKB105, a derivative of B. subtilis 168 with a restored ability to synthesize surfactin and other nonribosomal secondary metabolites, revealed that 176 genes were differentially expressed after exposing the Bacillus cells to rice seedlings. Most of them are likely to be involved in plant-bacteria interactions [6]. In recent years; several studies were performed with plant-associated B. amyloliquefaciens FZB42, a plant growth promoting bacterium with industrial importance [3]. A first transcriptome analysis about gene expression in response to maize root exudates revealed that majority of the genes possibly involved in plant plant-bacterium interactions was up-regulated when FZB42 was exposed to root exudates [7]. Extracellular proteome maps of FZB42 generated during the late exponential and stationary phase suggested that B. amyloliquefaciens protects plants against disease by eliciting innate immunity. Interestingly, the protein with the highest fold change in the presence of maize root exudates was acetoacetate synthase, an enzyme involved in the synthesis of the volatile acetoin, known as an inducer of systemic resistance against plant pathogens and as trigger of plant growth [8]. The effect of root exudates collected from maize plants grown under nitrogen (N), phosphate (P), iron (Fe) and potassium (K) deficiencies on the transcriptome of FZB42 was evaluated. Exudates from N-deprived maize triggered a general stress response in FZB42 in the exponential growth phase, which was evidenced by the suppression of numerous genes involved in protein synthesis. Global transcriptional changes in FZB42 elicited by nutrient deficient maize exudates were significantly correlated with concentrations of the amino acids aspartate, valine and glutamate in root exudates [9]. Plants colonized by root-colonizing Bacilli are affected in their gene expression pattern. Transcript profiling of Brassica seedlings primed with B. amyloliquefaciens revealed that a systemic gene expression in leaves was provoked by the bacterium [10]. Similar to FZB42, the environmental B. subtilis FB 17 acts as a beneficial rhizobacterium. When exposed to Arabidopsis roots it affects gene expression in the host plant. Genes up-regulated include auxin-regulated genes as well as genes involved in metabolism, stress response, and plant defense [11]. Taken together, value of global gene expression studies on the transcript and protein level for a deeper understanding of interactions between beneficial Bacilli and their host plants has been impressively verified. It is to expect that in future, analysis of the primary transcriptome by the differential RNA-seq (dRNA-seq) approach [12] will become crucial for analysing the global gene response of plant-associated Bacilli during colonizing plant roots.
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