Dataset Information

High-Throughput Identification of Antimicrobial Peptides from Amphibious Mudskippers.

ABSTRACT: Widespread existence of antimicrobial peptides (AMPs) has been reported in various animals with comprehensive biological activities, which is consistent with the important roles of AMPs as the first line of host defense system. However, no big-data-based analysis on AMPs from any fish species is available. In this study, we identified 507 AMP transcripts on the basis of our previously reported genomes and transcriptomes of two representative amphibious mudskippers, Boleophthalmus pectinirostris (BP) and Periophthalmus magnuspinnatus (PM). The former is predominantly aquatic with less time out of water, while the latter is primarily terrestrial with extended periods of time on land. Within these identified AMPs, 449 sequences are novel; 15 were reported in BP previously; 48 are identically overlapped between BP and PM; 94 were validated by mass spectrometry. Moreover, most AMPs presented differential tissue transcription patterns in the two mudskippers. Interestingly, we discovered two AMPs, hemoglobin ?1 and amylin, with high inhibitions on Micrococcus luteus. In conclusion, our high-throughput screening strategy based on genomic and transcriptomic data opens an efficient pathway to discover new antimicrobial peptides for ongoing development of marine drugs.

SUBMITTER: Yi Y

PROVIDER: S-EPMC5706053 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature

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High-Throughput Identification of Antimicrobial Peptides from Amphibious Mudskippers.

Yi Yunhai Y You Xinxin X Bian Chao C Chen Shixi S Lv Zhao Z Qiu Limei L Shi Qiong Q

Marine drugs 20171122 11

Widespread existence of antimicrobial peptides (AMPs) has been reported in various animals with comprehensive biological activities, which is consistent with the important roles of AMPs as the first line of host defense system. However, no big-data-based analysis on AMPs from any fish species is available. In this study, we identified 507 AMP transcripts on the basis of our previously reported genomes and transcriptomes of two representative amphibious mudskippers, <i>Boleophthalmus pectinirostr ...[more]

PMID: 29165344

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Project description:BackgroundAnti-microbial peptides (AMPs), naturally encoded by genes and generally containing 12-100 amino acids, are crucial components of the innate immune system and can protect the host from various pathogenic bacteria and viruses. In recent years, the widespread use of antibiotics has resulted in the rapid growth of antibiotic-resistant microorganisms that often induce critical infection and pathogenesis. Recently, the advent of high-throughput technologies has led molecular biology into a data surge in both the amount and scope of data. For instance, next-generation sequencing technology has been applied to generate large-scale sequencing reads from foods, water, soil, air, and specimens to identify microbiota and their functions based on metagenomics and metatranscriptomics, respectively. In addition, oolong tea is partially fermented and is the most widely produced tea in Taiwan. Many studies have shown the benefits of oolong tea in inhibiting obesity, reducing dental plaque deposition, antagonizing allergic immune responses, and alleviating the effects of aging. However, the microbes and their functions present in oolong tea remain unknown.ResultsTo understand the relationship between Taiwanese oolong teas and bacterial communities, we designed a novel bioinformatics scheme to identify AMPs and their functional types based on metagenomics and metatranscriptomic analysis of high-throughput transcriptome data. Four types of oolong teas (Dayuling tea, Alishan tea, Jinxuan tea, and Oriental Beauty tea) were subjected to 16S ribosomal DNA and total RNA extraction and sequencing. Metagenomics analysis results revealed that Oriental Beauty tea exhibited greater bacterial diversity than other teas. The most common bacterial families across all tea types were Bacteroidaceae (21.7%), Veillonellaceae (22%), and Fusobacteriaceae (12.3%). Metatranscriptomics analysis results revealed that the dominant bacteria species across all tea types were Escherichia coli, Bacillus subtilis, and Chryseobacterium sp. StRB126, which were subjected to further functional analysis. A total of 8194 (6.5%), 26,220 (6.1%), 5703 (5.8%), and 106,183 (7.8%) reads could be mapped to AMPs.ConclusionWe found that the distribution of anti-gram-positive and anti-gram-negative AMPs is highly correlated with the distribution of gram-positive and gram-negative bacteria in Taiwanese oolong tea samples.

Dataset Information

High-Throughput Identification of Antimicrobial Peptides from Amphibious Mudskippers.

Publications

High-Throughput Identification of Antimicrobial Peptides from Amphibious Mudskippers.

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