Unknown,Transcriptomics,Genomics,Proteomics

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Infection of apple by Apple stem grooving virus leads to extensive alterations in gene expression patterns but no disease symptoms

ABSTRACT: To understand the molecular basis of viral diseases, transcriptome profiling has been widely used to correlate host gene expression change patterns with disease symptoms during viral infection in many plant hosts. We used infection of apple by Apple stem grooving virus (ASGV), which produces no disease symptoms, to assess the significance of host gene expression changes in disease development. We specifically asked the question whether such asymptomatic infection is attributed to limited changes in host gene expression. Using RNA-seq, we identified a total of 184 up-regulated and 136 down-regulated genes in apple shoot cultures permanently infected by ASGV in comparison with virus-free shoots cultures. As in most plant hosts showing disease symptoms during viral infection, these differentially expressed genes encode known or putative proteins involved in cell cycle, cell wall biogenesis, response to biotic and abiotic stress, development and fruit ripening, phytohormone function, metabolism, signal transduction, transcription regulation, translation, transport, and photosynthesis. Our data suggest that current approaches to correlate host gene expression changes under viral infection conditions to specific infection processes or disease symptom development, based on the interpretation of individual gene functions, have severe limitations. Integrative approaches that can take into account plant development stages, gene threshold levels as well as compensatory, synergistic and antagonistic effects may be necessary to develop a sound systems understanding of the biological significance of host gene expression changes during infection. Compare the transcript profiling of ASGV-infected asymptomatic apple planlets (AP-Vinfect) and virus-free apple plantlets (AP-Vfree) by deep sequencing using Illumina RNA-Seq to check whether lots of genes were modulated by ASGV infection.

ORGANISM(S): Malus domestica

SUBMITTER: Ting Ye

PROVIDER: E-GEOD-53825 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Infection of apple by apple stem grooving virus leads to extensive alterations in gene expression patterns but no disease symptoms.

Chen Shanyi S Ye Ting T Hao Lu L Chen Hui H Wang Shaojie S Fan Zaifeng Z Guo Liyun L Zhou Tao T

PloS one 20140415 4

To understand the molecular basis of viral diseases, transcriptome profiling has been widely used to correlate host gene expression change patterns with disease symptoms during viral infection in many plant hosts. We used infection of apple by Apple stem grooving virus (ASGV), which produces no disease symptoms, to assess the significance of host gene expression changes in disease development. We specifically asked the question of whether such asymptomatic infection is attributed to limited chan ...[more]

PMID: 24736405

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Project description:Woody plant material represents a vast renewable resource that has the potential to produce biofuels and other bio-based products with favourable net CO2 emissions1,2. Its potential has been demonstrated in a recent study that generated novel structural materials from flexible mouldable wood3. The study of viral infection in plants has largely focussed on detrimental symptoms, such as leaf yellowing or cell death that result in reduced crop yields. Apple rubbery wood (ARW) disease is the result of a viral infection that causes woody stems to exhibit increased flexibility4. While ARW disease is associated with the presence of an RNA virus5 (ARWV), the mechanism underlying the development of its unique symptoms is not known. We demonstrate that ARWV symptoms arise from reduced lignification within the secondary cell wall of xylem fibres, while the mid-lamellae region and xylem ray cells are largely unaffected, and results in increased wood digestibility. Gene expression and proteomic data from symptomatic xylem clearly show the downregulation of phenylalanine ammonia lyase (PAL), the enzyme catalysing the first committed step in the phenylpropanoid pathway leading 2 to lignin biosynthesis. PAL downregulation is the likely cause of the decreased lignification, which is consistent with a large increase in soluble phenolics, including the lignin precursor phenylalanine, seen in symptomatic xylem. ARWV-infection results in the accumulation of many host-derived viral activated small interfering RNAs (vasiRNAs). PAL-derived vasiRNAs are among the most abundant vasiRNAs in symptomatic xylem and are likely the cause of reduced PAL activity. Apparently, the mechanism used by the virus to alter lignin exhibits similarities to the RNAi strategy that has been used to alter lignin in genetically modified trees to generate comparable improvements in wood properties6–8. CRISPR technology was recently used to increase yields in maize by introducing the naturally occurring waxy mutation into maize9. A similar biomimetic approach for biomass improvement based upon our understanding of ARWV symptoms offers a promising route to improve wood properties and provides important context for the genetic manipulation of trees.

Dataset Information

Infection of apple by Apple stem grooving virus leads to extensive alterations in gene expression patterns but no disease symptoms

Publications

Infection of apple by apple stem grooving virus leads to extensive alterations in gene expression patterns but no disease symptoms.

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