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ABSTRACT: RNA-Seq of Amaranthus tricolor

PROVIDER: PRJNA609229 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR11196359_1.fastq.gz	Fastqsanger.gz
	SRR11196359_2.fastq.gz	Fastqsanger.gz
	SRR11196360_1.fastq.gz	Fastqsanger.gz
	SRR11196360_2.fastq.gz	Fastqsanger.gz
	SRR11196361_1.fastq.gz	Fastqsanger.gz

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Amaranthus tricolor cultivar:Dahong

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Mass spectrometry guided by transcriptomics reveals multiple classes of predicted antimicrobial peptides in Amaranthus tricolor

Project description:Traditional medicinal plants are rich reservoirs of antimicrobial agents, including antimicrobial peptides (AMPs). Herein, Amaranthus tricolor AMPs predicted in silico are identified via proteomics profiling. Bottom-up proteomics identified seven novel peptides spanning three AMP classes including lipid transfer proteins, snakins and defensins. Characterization via top-down peptidomic analysis of Atr-SN1, Atr-DEF1, and Atr-LTP1 revealed unexpected proteolytic processing and enumerated disulfide bonds. These results highlight the potential for integrating AMP prediction algorithms with complementary -omics approaches to accelerate characterization of biologically relevant AMP peptidoforms.

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PepSAVI-MS reveals proline-rich antimicrobial peptide in Amaranthus tricolor

Project description:PepSAVI-MS, a mass spectrometry-based peptidomics pipeline, was implemented for antimicrobial peptide (AMP) discovery in the medicinal plant Amaranthus tricolor. This investigation revealed a novel 1.7 kDa AMP, deemed Atr-AMP1. Initial efforts to determine the sequence of Atr-AMP1 utilized chemical derivatization and enzymatic digestion to provide information about specific residues and post-translational modifications. EThcD (electron-transfer/higher-energy collision dissociation) produced extensive backbone fragmentation and facilitated de novo sequencing, the results of which were consistent with orthogonal characterization experiments. Additionally, multistage HCD (higher-energy collisional dissociation) facilitated discrimination between isobaric leucine and isoleucine. These results revealed a positively-charged proline-rich peptide present in a heterogeneous population of multiple peptidoforms, possessing several post-translational modifications including a disulfide bond, methionine oxidation, and proline hydroxylation.

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