title: Global Transcriptome Analysis of Gracilaria changii (Rhodophyta) in Response to Agarolytic Enzyme and Bacterium.
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.
authors.affiliation: Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
authors.forename: Ee-Leen
authors.initials: EL
authors.lastname: Lim
authors.affiliation: Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
authors.forename: Rouh-San
authors.initials: RS
authors.lastname: Siow
authors.affiliation: Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
authors.forename: Raha
authors.initials: R
authors.lastname: Abdul Rahim
authors.affiliation: Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia. clho@upm.edu.my.|Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia. clho@upm.edu.my.
authors.forename: Chai-Ling
authors.initials: CL
authors.lastname: Ho
mesh_terms: D000362:Agar / Q000378:metabolism; D020418:Algal Proteins / Q000235:genetics / Q000378:metabolism; D000818:Animals; D001419:Bacteria / Q000201:enzymology; D001426:Bacterial Proteins / Q000378:metabolism*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006026:Glycoside Hydrolases / Q000378:metabolism*; D044724:Gracilaria / Q000235:genetics* / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D006868:Hydrolysis; D053858:Metabolic Networks and Pathways / Q000235:genetics; D058977:Molecular Sequence Annotation; D060888:Real-Time Polymerase Chain Reaction; D012624:Seaweed / Q000235:genetics* / Q000378:metabolism; D013312:Stress, Physiological; D059467:Transcriptome
chemical_list: D020418:Algal Proteins; D001426:Bacterial Proteins; D000362:Agar; D006026:Glycoside Hydrolases; C019624:agarase
keywords: Agarase; Agarolytic bacterium; Defense response; Gene expression; High-throughput sequencing; Quantitative reverse transcription real-time PCR