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Global Transcriptome Analysis of Gracilaria changii (Rhodophyta) in Response to Agarolytic Enzyme and Bacterium

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Abstract

Many bacterial epiphytes of agar-producing seaweeds secrete agarase that degrade algal cell wall matrix into oligoagars which elicit defense-related responses in the hosts. The molecular defense responses of red seaweeds are largely unknown. In this study, we surveyed the defense-related transcripts of an agarophyte, Gracilaria changii, treated with β-agarase through next generation sequencing (NGS). We also compared the defense responses of seaweed elicited by agarase with those elicited by an agarolytic bacterium isolated from seaweed, by profiling the expression of defense-related genes using quantitative reverse transcription real-time PCR (qRT-PCR). NGS detected a total of 391 differentially expressed genes (DEGs) with a higher abundance (>2-fold change with a p value <0.001) in the agarase-treated transcriptome compared to that of the non-treated G. changii. Among these DEGs were genes related to signaling, bromoperoxidation, heme peroxidation, production of aromatic amino acids, chorismate, and jasmonic acid. On the other hand, the genes encoding a superoxide-generating NADPH oxidase and related to photosynthesis were downregulated. The expression of these DEGs was further corroborated by qRT-PCR results which showed more than 90 % accuracy. A comprehensive analysis of their gene expression profiles between 1 and 24 h post treatments (hpt) revealed that most of the genes analyzed were consistently upregulated or downregulated by both agarase and agarolytic bacterial treatments, indicating that the defense responses induced by both treatments are highly similar except for genes encoding vanadium bromoperoxidase and animal heme peroxidase. Our study has provided the first glimpse of the molecular defense responses of G. changii to agarase and agarolytic bacterial treatments.

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Abbreviations

ABS1:

Agarolytic bacteria strain 1

AO:

Ascorbate oxidase

BLASTN:

Basic local alignment search tool

cfu:

Colony-forming units

DAHP:

3-deoxy-D-arabino-heptulosonate-7-phosphate

DEGs:

Differentially expressed genes

ESTs:

Expressed sequence tags

EPSP:

5-enolpyruvylshikimate-3-phosphate

hpt:

Hour(s) post treatment

JA:

Jasmonic acid

MAMPs:

Microbial associated molecular patterns

MAPK:

Mitogen-activated protein kinase

MeJA:

Methyl jasmonate

MIMP:

Microbe-induced molecular pattern

NCBI:

National Center for Biotechnology Information

NGS:

Next generation sequencing

Phe:

L-phenylalanine

qRT real-time PCR:

Quantitative reverse transcription real-time PCR

ROS:

Reactive oxygen species

SSW:

Synthetic seawater

Trp:

L-tryptophan

Tyr:

L-tyrosine

VBPO:

Vanadium-dependent bromoperoxidase

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Acknowledgments

This project was funded by Fundamental Research Grant Scheme, No: 01-04-10-769FR from the Ministry of Higher Education (MOHE) of Malaysia. Lim E-L and Siow R-S were supported by Universiti Putra Malaysia under the Graduate Research Fellowship. We thank Mr. Lee W-W for helpful discussion in mRNA-seq analysis. Constructive comments from anonymous reviewers are highly appreciated.

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Authors and Affiliations

  1. Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia

    Ee-Leen Lim, Rouh-San Siow, Raha Abdul Rahim & Chai-Ling Ho

  2. Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia

    Chai-Ling Ho

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  1. Ee-Leen Lim
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Online Resource Table S1

DEGs of G. changii treated with agarose in comparison to untreated G. changii. (XLSX 25 kb)

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Lim, EL., Siow, RS., Abdul Rahim, R. et al. Global Transcriptome Analysis of Gracilaria changii (Rhodophyta) in Response to Agarolytic Enzyme and Bacterium. Mar Biotechnol 18, 189–200 (2016). https://doi.org/10.1007/s10126-015-9680-6

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