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Panteleev PV, Safronova VN, Duan S, Komlev AS, Bolosov IA, Kruglikov RN, Kombarova TI, Korobova OV, Pereskokova ES, Borzilov AI, Dyachenko IA, Shamova OV, Huang Y, Shi Q, Ovchinnikova TV. Novel BRICHOS-Related Antimicrobial Peptides from the Marine Worm Heteromastus filiformis: Transcriptome Mining, Synthesis, Biological Activities, and Therapeutic Potential. Mar Drugs 2023; 21:639. [PMID: 38132960 PMCID: PMC10745061 DOI: 10.3390/md21120639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
Marine polychaetes represent an extremely rich and underexplored source of novel families of antimicrobial peptides (AMPs). The rapid development of next generation sequencing technologies and modern bioinformatics approaches allows us to apply them for characterization of AMP-derived genes and the identification of encoded immune-related peptides with the aid of genome and transcriptome mining. Here, we describe a universal bioinformatic approach based on the conserved BRICHOS domain as a search query for the identification of novel structurally unique AMP families in annelids. In this paper, we report the discovery of 13 novel BRICHOS-related peptides, ranging from 18 to 91 amino acid residues in length, in the cosmopolitan marine worm Heteromastus filiformis with the assistance of transcriptome mining. Two characteristic peptides with a low homology in relation to known AMPs-the α-helical amphiphilic linear peptide, consisting of 28 amino acid residues and designated as HfBRI-28, and the 25-mer β-hairpin peptide, specified as HfBRI-25 and having a unique structure stabilized by two disulfide bonds-were obtained and analyzed as potential antimicrobials. Interestingly, both peptides showed the ability to kill bacteria via membrane damage, but mechanisms of their action and spectra of their activity differed significantly. Being non-cytotoxic towards mammalian cells and stable to proteolysis in the blood serum, HfBRI-25 was selected for further in vivo studies in a lethal murine model of the Escherichia coli infection, where the peptide contributed to the 100% survival rate in animals. A high activity against uropathogenic strains of E. coli (UPEC) as well as a strong ability to kill bacteria within biofilms allow us to consider the novel peptide HfBRI-25 as a promising candidate for the clinical therapy of urinary tract infections (UTI) associated with UPEC.
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Affiliation(s)
- Pavel V. Panteleev
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.P.); (V.N.S.); (S.D.); (I.A.B.); (R.N.K.)
| | - Victoria N. Safronova
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.P.); (V.N.S.); (S.D.); (I.A.B.); (R.N.K.)
| | - Shuting Duan
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.P.); (V.N.S.); (S.D.); (I.A.B.); (R.N.K.)
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen 518081, China; (Y.H.); (Q.S.)
| | - Alexey S. Komlev
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, 197022 St. Petersburg, Russia; (A.S.K.); (O.V.S.)
| | - Ilia A. Bolosov
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.P.); (V.N.S.); (S.D.); (I.A.B.); (R.N.K.)
| | - Roman N. Kruglikov
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.P.); (V.N.S.); (S.D.); (I.A.B.); (R.N.K.)
| | - Tatiana I. Kombarova
- State Research Center for Applied Microbiology & Biotechnology (SRCAMB), 142279 Obolensk, Russia; (T.I.K.); (O.V.K.); (E.S.P.); (A.I.B.)
| | - Olga V. Korobova
- State Research Center for Applied Microbiology & Biotechnology (SRCAMB), 142279 Obolensk, Russia; (T.I.K.); (O.V.K.); (E.S.P.); (A.I.B.)
| | - Eugenia S. Pereskokova
- State Research Center for Applied Microbiology & Biotechnology (SRCAMB), 142279 Obolensk, Russia; (T.I.K.); (O.V.K.); (E.S.P.); (A.I.B.)
| | - Alexander I. Borzilov
- State Research Center for Applied Microbiology & Biotechnology (SRCAMB), 142279 Obolensk, Russia; (T.I.K.); (O.V.K.); (E.S.P.); (A.I.B.)
| | - Igor A. Dyachenko
- The Branch of M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Olga V. Shamova
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, 197022 St. Petersburg, Russia; (A.S.K.); (O.V.S.)
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen 518081, China; (Y.H.); (Q.S.)
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen 518081, China; (Y.H.); (Q.S.)
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518057, China
| | - Tatiana V. Ovchinnikova
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.P.); (V.N.S.); (S.D.); (I.A.B.); (R.N.K.)
- Department of Biotechnology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
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Kobayashi G. Buried treasure in a public repository: Mining mitochondrial genes of 32 annelid species from sequence reads deposited in the Sequence Read Archive (SRA). PeerJ 2023; 11:e16446. [PMID: 38047014 PMCID: PMC10693233 DOI: 10.7717/peerj.16446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/21/2023] [Indexed: 12/05/2023] Open
Abstract
Background The mitochondrial genomes (mitogenomes) of metazoans generally include the same set of protein-coding genes, which ensures the homology of mitochondrial genes between species. The mitochondrial genes are often used as reference data for species identification based on genetic data (DNA barcoding). The need for such reference data has been increasing due to the application of environmental DNA (eDNA) analysis for environmental assessments. Recently, the number of publicly available sequence reads obtained with next-generation sequencing (NGS) has been increasing in the public database (the NCBI Sequence Read Archive, SRA). Such freely available NGS reads would be promising sources for assembling mitochondrial protein-coding genes (mPCGs) of organisms whose mitochondrial genes are not available in GenBank. The present study aimed to assemble annelid mPCGs from raw data deposited in the SRA. Methods The recent progress in the classification of Annelida was briefly introduced. In the present study, the mPCGs of 32 annelid species of 19 families in clitellates and allies in Sedentaria (echiurans and polychaetes) were newly assembled from the reads deposited in the SRA. Assembly was performed with a recently published pipeline mitoRNA, which includes cycles of Bowtie2 mapping and Trinity assembly. Assembled mPCGs were deposited in GenBank as Third Party Data (TPA) data. A phylogenetic tree was reconstructed with maximum likelihood (ML) analysis, together with other mPCGs deposited in GenBank. Results and Discussion mPCG assembly was largely successful except for Travisia forbesii; only four genes were detected from the assembled contigs of the species probably due to the reads targeting its parasite. Most genes were largely successfully obtained, whereas atp8, nad2, and nad4l were only successful in 22-24 species. The high nucleotide substitution rates of these genes might be relevant to the failure in the assembly although nad6, which showed a similarly high substitution rate, was successfully assembled. Although the phylogenetic positions of several lineages were not resolved in the present study, the phylogenetic relationships of some polychaetes and leeches that were not inferred by transcriptomes were well resolved probably due to a more dense taxon sampling than previous phylogenetic analyses based on transcriptomes. Although NGS data are generally better sources for resolving phylogenetic relationships of both higher and lower classifications, there are ensuring needs for specific loci of the mitochondrial genes for analyses that do not require high resolutions, such as DNA barcoding, eDNA, and phylogenetic analysis among lower taxa. Assembly from publicly available NGS reads would help design specific primers for the mitochondrial gene sequences of species, whose mitochondrial genes are hard to amplify by Sanger sequencing using universal primers.
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Affiliation(s)
- Genki Kobayashi
- Research Center for Creative Partnerships, Ishinomaki Senshu University, Ishinomaki, Miyagi, Japan
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Song M, Wang J, Wang Y, Hu R, Wang L, Guo Z, Jiang Z, Liang Z. Response mechanism of meiofaunal communities to multi-type of artificial reef habitats from the perspective of high-throughput sequencing technology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160927. [PMID: 36543272 DOI: 10.1016/j.scitotenv.2022.160927] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 12/04/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
Multiple types of artificial reefs have been widely deployed in the coast of northern Yellow Sea, which can enhance fishery resources, restore coastal habitats and improve the marine environment. Meiofauna plays important ecological roles in marine ecosystem, but the response mechanism of meiofaunal community to different types of artificial reef is still poorly understood. In this study, we characterized the meiofaunal communities of concrete artificial reef habitat (CAR), rocky artificial reef habitat (RAR), ship artificial reef habitat (SAR) and adjacent natural habitat (NH) using 18S rRNA gene high-throughput sequencing technology, and explored the relationship of community-environment. The results showed that the diversity and community structure of meiofauna differed significantly on both spatial and temporal scales. Spatial differences were mainly contributed to the flow field effects and biological effects generated by artificial habitats, while temporal differences were driven by temperature (T) and dissolved oxygen (DO). The dominant taxa of meiofauna included arthropods, annelids, platyhelminths and nematodes. Platyhelminths were mainly positively influenced by artificial habitats but annelids were the opposite. Co-occurrence network analysis revealed that NH was more sensitive to environmental change than artificial habitat, while the performance of CAR and SAR were more stable. These results indicated that meiofauna can respond accordingly to different types of artificial habitats, and could be superimposed over the normal seasonal effects. The current study could provide fundamental data for understanding the response mechanism of meiofaunal community to different types of artificial habitats and a reference for assessments of the impact of artificial reefs on the marine environment.
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Affiliation(s)
- Minpeng Song
- Marine College, Shandong University, Weihai, Shandong 264209, China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, Shandong 264209, China
| | - Jiahao Wang
- Marine College, Shandong University, Weihai, Shandong 264209, China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, Shandong 264209, China
| | - Yuxin Wang
- Marine College, Shandong University, Weihai, Shandong 264209, China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, Shandong 264209, China
| | - Renge Hu
- Marine College, Shandong University, Weihai, Shandong 264209, China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, Shandong 264209, China
| | - Lu Wang
- Marine College, Shandong University, Weihai, Shandong 264209, China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, Shandong 264209, China
| | - Zhansheng Guo
- Marine College, Shandong University, Weihai, Shandong 264209, China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, Shandong 264209, China
| | - Zhaoyang Jiang
- Marine College, Shandong University, Weihai, Shandong 264209, China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, Shandong 264209, China.
| | - Zhenlin Liang
- Marine College, Shandong University, Weihai, Shandong 264209, China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, Shandong 264209, China.
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First Report of a Paucibranchia (Polychaeta, Eunicidae) Species without Lateral Palps in Korean Subtidal Waters, with Genetic Evidence for Its Taxonomic Position. DIVERSITY 2022. [DOI: 10.3390/d14121131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
An undescribed species belonging to the family Eunicidae was detected in a sublittoral habitat of the southern coast of Korea. This Korean eunicid species was initially thought to belong to the genus Lysidice based on its general appearance, including the absence of prostomial lateral palps and peristomial cirri. However, a more detailed characterization of the morphological features of the maxillae and mandible coupled with mtCOI and 18S rRNA gene sequence analyses confirmed that this species is a member of the genus Paucibranchia. The absence of lateral palps found in the intact adult specimens with 153 segments is a unique feature not previously reported in species belonging to Paucibranchia. Thus, the new species, Paucibranchia triantennata sp. nov., can be easily distinguished from other known congeneric species. Except for the absence of lateral palps, P. triantennata sp. nov. resembled P. conferta, P. gathofi, and P. patriciae in the shape of the prostomium, brief location and shape of branchiae, and absence of compound spinigers. However, P. triantennata could be clearly distinguished from these species by the shorter prostomial antennae, a large number of subacicular hooks, and the morphological features of the maxillae and compound falcigers.
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