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Paiva ALB, de Souza Santos JH, Queiroz Machado VP, Santos DM, Diniz MRV, Guerra-Duarte C. Unveiling hidden toxin diversity: Discovery of novel venom components through manual curation of highly expressed sequences annotated as "no hits" in Phoneutria nigriventer spider venom gland transcriptome. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 49:101155. [PMID: 37952503 DOI: 10.1016/j.cbd.2023.101155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/26/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023]
Abstract
Spider venoms have evolved over thousands of years, optimizing feeding and defense mechanisms. Venom components show pharmacological and biotechnological potential, rising interest in their study. However, the isolation of spider toxins for experimental evaluation poses significant challenges. To address this, transcriptomic analysis combined with computational tools has emerged as an appealing approach to characterizing spider venoms. However, many sequences remain unidentified after automatic annotation. In this study, we manually curated a subset of previously unannotated sequences from the Phoneutria nigriventer transcriptome and identified new putative venom components. Our manual analysis revealed 29 % of the analyzed sequences were potential venom components, 29 % hypothetical/uncharacterized proteins, and 17 % cellular function proteins. Only 25 % of the originally unannotated dataset remained without any identification. Most reclassified components were cysteine-rich peptides, including 23 novel putative toxins. We also found glycine-rich peptides (GRP), corroborating the previous description of GRPs in Phoneutria pertyi venom glands. Furthermore, to emphasize the recurrence of the lack of annotation in spider venom glands transcripts, we provide a survey of the percentage of unidentified sequences in several published spider venom transcriptomics studies. In conclusion, our study highlights the importance of manual curation in uncovering novel venom components and underscores the need for improved annotation strategies to fully exploit the medical and biotechnological potential of spider venoms.
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Affiliation(s)
| | | | | | - Daniel Moreira Santos
- Campus Centro-Oeste, Universidade Federal de São João Del-Rey, Divinópolis, Minas Gerais, Brazil
| | | | - Clara Guerra-Duarte
- Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil. https://twitter.com/@claraguerrad
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2
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Miyamoto JG, Kitano ES, Zelanis A, Nachtigall PG, Junqueira-de-Azevedo I, Sant'Anna SS, Lauria da Silva R, Bersanetti PA, Carmona AK, Barbosa Pereira PJ, Serrano SMT, Vilela Oliva ML, Tashima AK. A novel metalloproteinase-derived cryptide from Bothrops cotiara venom inhibits angiotensin-converting enzyme activity. Biochimie 2024; 216:90-98. [PMID: 37839625 DOI: 10.1016/j.biochi.2023.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/06/2023] [Accepted: 10/13/2023] [Indexed: 10/17/2023]
Abstract
Snake venoms are primarily composed of proteins and peptides, which selectively interact with specific molecular targets, disrupting prey homeostasis. Identifying toxins and the mechanisms involved in envenoming can lead to the discovery of new drugs based on natural peptide scaffolds. In this study, we used mass spectrometry-based peptidomics to sequence 197 peptides in the venom of Bothrops cotiara, including a novel 7-residue peptide derived from a snake venom metalloproteinase. This peptide, named Bc-7a, features a pyroglutamic acid at the N-terminal and a PFR motif at the C-terminal, homologous to bradykinin. Using FRET (fluorescence resonance energy transfer) substrate assays, we demonstrated that Bc-7a strongly inhibits the two domains of angiotensin converting enzyme (Ki < 1 μM). Our findings contribute to the repertoire of biologically active peptides from snake venoms capable of inhibiting angiotensin-converting enzyme (ACE), beyond current known structural motifs and precursors. In summary, we report a novel snake venom peptide with ACE inhibitory activity, suggesting its potential contribution to the hypotensive effect observed in envenomation.
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Affiliation(s)
- Jackson Gabriel Miyamoto
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo, Brazil
| | - Eduardo Shigueo Kitano
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signaling, Butantan Institute, SP, 05503-900, São Paulo, Brazil
| | - André Zelanis
- Functional Proteomics Laboratory, Department of Science and Technology, Federal University of São Paulo (ICT-UNIFESP), São José dos Campos, Brazil
| | - Pedro Gabriel Nachtigall
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signaling, Butantan Institute, SP, 05503-900, São Paulo, Brazil
| | - Inácio Junqueira-de-Azevedo
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signaling, Butantan Institute, SP, 05503-900, São Paulo, Brazil
| | | | - Rogério Lauria da Silva
- Department of Biophysics, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo, Brazil
| | | | | | - Pedro José Barbosa Pereira
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal; i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Solange M T Serrano
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signaling, Butantan Institute, SP, 05503-900, São Paulo, Brazil
| | - Maria Luiza Vilela Oliva
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo, Brazil
| | - Alexandre Keiji Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo, Brazil.
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3
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Nishiduka ES, Lomazi RL, da Silva PI, Tashima AK. Identification of Peptides in Spider Venom Using Mass Spectrometry. Methods Mol Biol 2024; 2758:331-340. [PMID: 38549023 DOI: 10.1007/978-1-0716-3646-6_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Spider venoms are composed of hundreds of proteins and peptides. Several of these venom toxins are cysteine-rich peptides in the mass range of 3-9 kDa. Small peptides (<3 kDa) can be fully characterized by mass spectrometry analysis, while proteins are generally identified by the bottom-up approach in which proteins are first digested with trypsin to generate shorter peptides for MS/MS characterization. In general, it is sufficient for protein identification to sequence two or more peptides, but for venom peptidomics it is desirable to completely elucidate peptide sequences and the number of disulfide bonds in the molecules. In this chapter, we describe a methodology to completely sequence and determine the number of disulfide bonds of spider venom peptides in the mass range of 3-9 kDa by multiple enzyme digestion, mass spectrometry of native and digested peptides, de novo analysis, and sequence overlap alignment.
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Affiliation(s)
- Erika S Nishiduka
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Rafael L Lomazi
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Pedro I da Silva
- Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, SP, Brazil
| | - Alexandre K Tashima
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
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4
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Guo R, Guo G, Wang A, Xu G, Lai R, Jin H. Spider-Venom Peptides: Structure, Bioactivity, Strategy, and Research Applications. Molecules 2023; 29:35. [PMID: 38202621 PMCID: PMC10779620 DOI: 10.3390/molecules29010035] [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: 10/16/2023] [Revised: 11/30/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024] Open
Abstract
Spiders (Araneae), having thrived for over 300 million years, exhibit remarkable diversity, with 47,000 described species and an estimated 150,000 species in existence. Evolving with intricate venom, spiders are nature's skilled predators. While only a small fraction of spiders pose a threat to humans, their venoms contain complex compounds, holding promise as drug leads. Spider venoms primarily serve to immobilize prey, achieved through neurotoxins targeting ion channels. Peptides constitute a major part of these venoms, displaying diverse pharmacological activities, and making them appealing for drug development. Moreover, spider-venom peptides have emerged as valuable tools for exploring human disease mechanisms. This review focuses on the roles of spider-venom peptides in spider survival strategies and their dual significance as pharmaceutical research tools. By integrating recent discoveries, it provides a comprehensive overview of these peptides, their targets, bioactivities, and their relevance in spider survival and medical research.
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Affiliation(s)
- Ruiyin Guo
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; (R.G.)
| | - Gang Guo
- The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), Kunming 650118, China;
| | - Aili Wang
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; (R.G.)
| | - Gaochi Xu
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; (R.G.)
| | - Ren Lai
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; (R.G.)
- Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, Kunming-Primate Research Center, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Sino-African Joint Research Center and Engineering Laboratory of Peptides, Kunming Institute of Zoology, Kunming 650107, China
| | - Hui Jin
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; (R.G.)
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5
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Yang M, Huan W, Zhang G, Li J, Xia F, Durrani R, Zhao W, Lu J, Peng X, Gao F. Identification of Protein Quality Markers in Toad Venom from Bufo gargarizans. Molecules 2023; 28:molecules28083628. [PMID: 37110862 PMCID: PMC10141085 DOI: 10.3390/molecules28083628] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/05/2023] [Accepted: 04/09/2023] [Indexed: 04/29/2023] Open
Abstract
Toad venom is a traditional Chinese medicine with high medicinal value. The existing quality evaluation standards of toad venom have obvious limitations because of the lack of research on proteins. Thus, it is necessary to screen suitable quality markers and establish appropriate quality evaluation methods for toad venom proteins to guarantee their safety and efficacy in clinical applications. SDS-PAGE, HPLC, and cytotoxicity assays were used to analyze differences in protein components of toad venom from different areas. Functional proteins were screened as potential quality markers by proteomic and bioinformatic analyses. The protein components and small molecular components of toad venom were not correlated in content. Additionally, the protein component had strong cytotoxicity. Proteomics analysis showed that 13 antimicrobial proteins, four anti-inflammatory and analgesic proteins, and 20 antitumor proteins were differentially expressed extracellular proteins. A candidate list of functional proteins was coded as potential quality markers. Moreover, Lysozyme C-1, which has antimicrobial activity, and Neuropeptide B (NPB), which has anti-inflammatory and analgesic activity, were identified as potential quality markers for toad venom proteins. Quality markers can be used as the basis of quality studies of toad venom proteins and help to construct and improve safe, scientific, and comprehensive quality evaluation methods.
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Affiliation(s)
- Meiyun Yang
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Weiwei Huan
- Zhejiang Provincial Key Laboratory of Chemical Utilization of Forestry Biomass, College of Chemistry and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China
| | - Guobing Zhang
- Department of Pharmacy, Zhejiang Province People's Hospital, Hangzhou 310014, China
| | - Jie Li
- Zhejiang Provincial Key Laboratory of Chemical Utilization of Forestry Biomass, College of Chemistry and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China
| | - Fengyan Xia
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 313000, China
| | - Rabia Durrani
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Wei Zhao
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Jidong Lu
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Xinmeng Peng
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Fei Gao
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
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6
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Zhang C, Li X, Xing Z, Zhong H, Yu D, Yu R, Deng X. Plasma metabolites-based design of long-acting peptides and their anticancer evaluation. Int J Pharm 2023; 631:122483. [PMID: 36509220 DOI: 10.1016/j.ijpharm.2022.122483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/26/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
Antimicrobial peptides (AMPs) are generally small cationic amphipathic peptides, which are thought to be ideal antineoplastic agents, owing to their favorable selectivity to cancer cells and the ability to overcome drug-resistance. In this study, an anticancer AMP (Mastoparan (INLKALAALAKKIL-NH2)) was selected as the lead compound and a series of Mastoparan derivatives were designed. Preliminary studies verified that an analogue of Mastoparan, KM8 (KLLKINLKALAALAKKIL-NH2), exhibited prominent selective antitumor effects. Instead, it presents a significant defect of metabolic instability, with a half-life in plasma of only about 0.5 h. Metabolite profiling of KM8 was performed and indicated the structure 9AL10 in peptide sequence could be the fragile site for KM8. Thus, the Aib (unnatural amnio acid) was employed to substitute the 9Ala residue in KM8, and generating a long-acting KM8 derivative, namely KM8-Aib. Further investigations revealed KM8-Aib possessed higher metabolic stability, more potent anticancer activity in vitro & in vivo, and lower toxicity. Therefore, KM8-Aib is suggested be a potential antimalignant agent that worthy of more in-depth study.
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Affiliation(s)
- Chenyu Zhang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China; Department of Pharmacy, Guangzhou Chest Hospital, 62 Hengzhigang Road, Guangzhou 510095, China
| | - Xiang Li
- Department of Pharmacy, Guangzhou Chest Hospital, 62 Hengzhigang Road, Guangzhou 510095, China
| | - Zhenjian Xing
- Department of Pharmacy, Guangzhou Chest Hospital, 62 Hengzhigang Road, Guangzhou 510095, China
| | - Honglan Zhong
- Department of Pharmacy, Guangzhou Chest Hospital, 62 Hengzhigang Road, Guangzhou 510095, China
| | - Dianbao Yu
- Analytical Applications Center, Shimadzu (China) Co., Ltd., Guangzhou Branch, 230 Gaotang Road, Guangzhou 510656, China
| | - Rui Yu
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China.
| | - Xin Deng
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China.
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7
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Barboza BR, Thomaz SMDO, Junior ADC, Espreafico EM, Miyamoto JG, Tashima AK, Camacho MF, Zelanis A, Roque-Barreira MC, da Silva TA. ArtinM Cytotoxicity in B Cells Derived from Non-Hodgkin's Lymphoma Depends on Syk and Src Family Kinases. Int J Mol Sci 2023; 24:ijms24021075. [PMID: 36674590 PMCID: PMC9863955 DOI: 10.3390/ijms24021075] [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: 12/08/2022] [Accepted: 12/15/2022] [Indexed: 01/09/2023] Open
Abstract
Receptors on the immune cell surface have a variety of glycans that may account for the immunomodulation induced by lectins, which have a carbohydrate recognition domain (CRD) that binds to monosaccharides or oligosaccharides in a specific manner. ArtinM, a D-mannose-binding lectin obtained from Artocarpus heterophyllus, has affinity for the N-glycans core. Immunomodulation by ArtinM toward the Th1 phenotype occurs via its interaction with TLR2/CD14 N-glycans on antigen-presenting cells, as well as recognition of CD3γ N-glycans on murine CD4+ and CD8+ T cells. ArtinM exerts a cytotoxic effect on Jurkat human leukemic T-cell line and human myeloid leukemia cell line (NB4). The current study evaluated the effects of ArtinM on murine and human B cells derived from non-Hodgkin’s lymphoma. We found that murine B cells are recognized by ArtinM via the CRD, and the ArtinM stimulus did not augment the proliferation rate or production of IL-2. However, murine B cell incubation with ArtinM augmented the rate of apoptosis, and this cytotoxic effect of ArtinM was also seen in human B cell-lines sourced from non-Hodgkin’s lymphoma Raji cell line. This cytotoxic effect was inhibited by the phosphatase activity of CD45 on Lck, and the protein kinases of the Src family contribute to cell death triggered by ArtinM.
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Affiliation(s)
- Bruno Rafael Barboza
- Laboratory of Immunochemistry and Glycobiology, Department of Cell and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo (FMRP/USP), Ribeirao Preto 14049-900, SP, Brazil
| | - Sandra Maria de Oliveira Thomaz
- Laboratory of Immunochemistry and Glycobiology, Department of Cell and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo (FMRP/USP), Ribeirao Preto 14049-900, SP, Brazil
| | - Airton de Carvalho Junior
- Laboratory of Cell and Molecular Biology of Cancer, Department of Cell and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo (FMRP/USP), Ribeirao Preto 14049-900, SP, Brazil
| | - Enilza Maria Espreafico
- Laboratory of Cell and Molecular Biology of Cancer, Department of Cell and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo (FMRP/USP), Ribeirao Preto 14049-900, SP, Brazil
| | - Jackson Gabriel Miyamoto
- Department of Biochemistry, Paulista School of Medicine, Federal University of São Paulo (EPM/UNIFESP), Sao Paulo 04021-001, SP, Brazil
| | - Alexandre Keiji Tashima
- Department of Biochemistry, Paulista School of Medicine, Federal University of São Paulo (EPM/UNIFESP), Sao Paulo 04021-001, SP, Brazil
| | - Maurício Frota Camacho
- Functional Proteomics Laboratory, Department of Science and Technology, Federal University of São Paulo (ICT-UNIFESP), São José dos Campos 04021-001, SP, Brazil
| | - André Zelanis
- Functional Proteomics Laboratory, Department of Science and Technology, Federal University of São Paulo (ICT-UNIFESP), São José dos Campos 04021-001, SP, Brazil
| | - Maria Cristina Roque-Barreira
- Laboratory of Immunochemistry and Glycobiology, Department of Cell and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo (FMRP/USP), Ribeirao Preto 14049-900, SP, Brazil
| | - Thiago Aparecido da Silva
- Laboratory of Immunotherapy of Invasive Fungal Infections, Department of Cell and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo (FMRP/USP), Ribeirao Preto 14049-900, SP, Brazil
- Correspondence: or ; Tel.: +55-16-3315-3049
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8
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Nishiduka ES, Abreu TF, Abukawa FM, Oliveira UC, Tardivo CEO, Nascimento SM, Meissner GO, Chaim OM, Juliano MA, Kitano ES, Zelanis A, Serrano SMT, da Silva PI, Junqueira-de-Azevedo IL, Nishiyama-Jr MY, Tashima AK. Multiomics Profiling of Toxins in the Venom of the Amazonian Spider Acanthoscurria juruenicola. J Proteome Res 2022; 21:2783-2797. [PMID: 36260604 DOI: 10.1021/acs.jproteome.2c00593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acanthoscurria juruenicola is an Amazonian spider described for the first time almost a century ago. However, little is known about their venom composition. Here, we present a multiomics characterization of A. juruenicola venom by a combination of transcriptomics, proteomics, and peptidomics approaches. Transcriptomics of female venom glands resulted in 93,979 unique assembled mRNA transcript encoding proteins. A total of 92 proteins were identified in the venom by mass spectrometry, including 14 mature cysteine-rich peptides (CRPs). Quantitative analysis showed that CRPs, cysteine-rich secretory proteins, metalloproteases, carbonic anhydrases, and hyaluronidase comprise >90% of the venom proteome. Relative quantification of venom toxins was performed by DIA and DDA, revealing converging profiles of female and male specimens by both methods. Biochemical assays confirmed the presence of active hyaluronidases, phospholipases, and proteases in the venom. Moreover, the venom promoted in vivo paralytic activities in crickets, consistent with the high concentration of CRPs. Overall, we report a comprehensive analysis of the arsenal of toxins of A. juruenicola and highlight their potential biotechnological and pharmacological applications. Mass spectrometry data were deposited to the ProteomeXchange Consortium via the PRIDE repository with the dataset identifier PXD013149 and via the MassIVE repository with the dataset identifier MSV000087777.
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Affiliation(s)
- Erika S Nishiduka
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo 04023-901, Brazil
| | - Thiago F Abreu
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo 04023-901, Brazil
| | - Fernanda Midori Abukawa
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signalig, CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Ursula C Oliveira
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signalig, CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Caio E O Tardivo
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo 04023-901, Brazil
| | - Soraia M Nascimento
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signalig, CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Gabriel O Meissner
- Department of Cell Biology, Federal University of Paraná, Curitiba 81531-980, Puerto Rico, Brazil
| | - Olga M Chaim
- Department of Cell Biology, Federal University of Paraná, Curitiba 81531-980, Puerto Rico, Brazil.,Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, California 92093, United States
| | - Maria A Juliano
- Department of Biophysics, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo 04021-001, Brazil
| | - Eduardo S Kitano
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signalig, CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
| | - André Zelanis
- Functional Proteomics Laboratory, Department of Science and Technology, Federal University of São Paulo, (ICT-UNIFESP), São José dos Campos 12231-280, Brazil
| | - Solange M T Serrano
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signalig, CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Pedro I da Silva
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signalig, CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Inácio L Junqueira-de-Azevedo
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signalig, CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Milton Y Nishiyama-Jr
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signalig, CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Alexandre K Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo 04023-901, Brazil
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9
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Analyzing the influence of age and sex in Bothrops pauloensis snake venom. Toxicon 2022; 214:78-90. [DOI: 10.1016/j.toxicon.2022.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/05/2022] [Accepted: 05/16/2022] [Indexed: 11/22/2022]
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10
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Antiviral Effects of Animal Toxins: Is There a Way to Drugs? Int J Mol Sci 2022; 23:ijms23073634. [PMID: 35408989 PMCID: PMC8998278 DOI: 10.3390/ijms23073634] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 12/18/2022] Open
Abstract
Viruses infect all types of organisms, causing viral diseases, which are very common in humans. Since viruses use the metabolic pathways of their host cells to replicate, they are difficult to eradicate without affecting the cells. The most effective measures against viral infections are vaccinations and antiviral drugs, which selectively inhibit the viral replication cycle. Both methods have disadvantages, which requires the development of new approaches to the treatment of viral diseases. In the study of animal venoms, it was found that, in addition to toxicity, venoms exhibit other types of biological activity, including an antiviral one, the first mention of which dates back to middle of the last century, but detailed studies of their antiviral activity have been conducted over the past 15 years. The COVID-19 pandemic has reinforced these studies and several compounds with antiviral activity have been identified in venoms. Some of them are very active and can be considered as the basis for antiviral drugs. This review discusses recent antiviral studies, the found compounds with high antiviral activity, and the possible mechanisms of their action. The prospects for using the animal venom components to create antiviral drugs, and the expected problems and possible solutions are also considered.
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11
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Marchi FC, Mendes-Silva E, Rodrigues-Ribeiro L, Bolais-Ramos LG, Verano-Braga T. Toxinology in the proteomics era: a review on arachnid venom proteomics. J Venom Anim Toxins Incl Trop Dis 2022; 28:20210034. [PMID: 35291269 PMCID: PMC8893269 DOI: 10.1590/1678-9199-jvatitd-2021-0034] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/01/2021] [Indexed: 11/22/2022] Open
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Macedo KWR, Costa LJDL, de Souza JO, de Vasconcelos IA, de Castro JS, de Santana CJC, Magalhães ACM, Castro MDS, Pires OR. Brazilian Theraphosidae: a toxicological point of view. J Venom Anim Toxins Incl Trop Dis 2021; 27:e20210004. [PMID: 34868282 PMCID: PMC8610171 DOI: 10.1590/1678-9199-jvatitd-2021-0004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/08/2021] [Indexed: 11/30/2022] Open
Abstract
The Theraphosidae family includes the largest number of species of the
Mygalomorphae infraorder, with hundreds of species currently catalogued.
However, there is a huge lack on physiologic and even ecologic information
available, especially in Brazil, which is the most biodiverse country in the
world. Over the years, spiders have been presented as a source of multiple
biologically active compounds with basic roles, such as primary defense against
pathogenic microorganisms or modulation of metabolic pathways and as specialized
hunters. Spider venoms also evolved in order to enable the capture of prey by
interaction with a diversity of molecular targets of interest, raising their
pharmaceutical potential for the development of new drugs. Among the activities
found in compounds isolated from venoms and hemocytes of Brazilian Theraphosidae
there are antimicrobial, antifungal, antiparasitic and antitumoral, as well as
properties related to proteinase action and neuromuscular blockage modulated by
ionic voltage-gated channel interaction. These characteristics are present in
different species from multiple genera, which is strong evidence of the
important role in spider survival. The present review aims to compile the main
results of studies from the last decades on Brazilian Theraphosidae with special
focus on results obtained with the crude venom or compounds isolated from both
venom and hemocytes, and their physiological and chemical characterization.
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Affiliation(s)
- Keven Wender Rodrigues Macedo
- Laboratory of Toxinology, Department of Physiological Sciences, Institute of Biology, University of Brasília (UnB), Brasília, DF, Brazil
| | - Lucas Jeferson de Lima Costa
- Laboratory of Toxinology, Department of Physiological Sciences, Institute of Biology, University of Brasília (UnB), Brasília, DF, Brazil
| | - Jéssica Oliveira de Souza
- Laboratory of Toxinology, Department of Physiological Sciences, Institute of Biology, University of Brasília (UnB), Brasília, DF, Brazil
| | - Isadora Alves de Vasconcelos
- Laboratory of Toxinology, Department of Physiological Sciences, Institute of Biology, University of Brasília (UnB), Brasília, DF, Brazil
| | - Jessica Schneider de Castro
- Laboratory of Toxinology, Department of Physiological Sciences, Institute of Biology, University of Brasília (UnB), Brasília, DF, Brazil
| | - Carlos José Correia de Santana
- Laboratory of Toxinology, Department of Physiological Sciences, Institute of Biology, University of Brasília (UnB), Brasília, DF, Brazil.,Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasília (UnB), Brasília, DF, Brazil
| | - Ana Carolina Martins Magalhães
- Laboratory of Toxinology, Department of Physiological Sciences, Institute of Biology, University of Brasília (UnB), Brasília, DF, Brazil
| | - Mariana de Souza Castro
- Laboratory of Toxinology, Department of Physiological Sciences, Institute of Biology, University of Brasília (UnB), Brasília, DF, Brazil.,Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasília (UnB), Brasília, DF, Brazil
| | - Osmindo Rodrigues Pires
- Laboratory of Toxinology, Department of Physiological Sciences, Institute of Biology, University of Brasília (UnB), Brasília, DF, Brazil
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13
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Tibery DV, de Souza ACB, Mourão CBF, do Nascimento JM, Schwartz EF. Purification and characterization of peptides Ap2, Ap3 and Ap5 (ω-toxins) from the venom of the Brazilian tarantula Acanthoscurria paulensis. Peptides 2021; 145:170622. [PMID: 34363923 DOI: 10.1016/j.peptides.2021.170622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 11/21/2022]
Abstract
Peptides isolated from spider venoms are of pharmacological interest due to their neurotoxic activity, acting on voltage-dependent ion channels present in different types of human body tissues. Three peptide toxins titled as Ap2, Ap3 and Ap5 were purified by RP-HPLC from Acanthoscurria paulensis venom. They were partially sequenced by MALDI In-source Decay method and their sequences were completed and confirmed by transcriptome analysis of the venom gland. The Ap2, Ap3 and Ap5 peptides have, respectively, 42, 41 and 46 amino acid residues, and experimental molecular masses of 4886.3, 4883.7 and 5454.7 Da, with the Ap2 peptide presenting an amidated C-terminus. Amongst the assayed channels - NaV1.1, NaV1.5, NaV1.7, CaV1.2, CaV2.1 and CaV2.2 - Ap2, Ap3 and Ap5 inhibited 20-30 % of CaV2.1 current at 1 μM concentration. Ap3 also inhibited sodium current in NaV1.1, Nav1.5 and Nav1.7 channels by 6.6 ± 1.91 % (p = 0.0276), 4.2 ± 1.09 % (p = 0.0185) and 16.05 ± 2.75 % (p = 0.0282), respectively. Considering that Ap2, Ap3 and Ap5 belong to the 'U'-unknown family of spider toxins, which has few descriptions of biological activity, the present work contributes to the knowledge of these peptides and demonstrates this potential as channel modulators.
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Affiliation(s)
- Diogo Vieira Tibery
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília, Brasília, Brazil
| | | | - Caroline Barbosa Farias Mourão
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília, Brasília, Brazil; Instituto Federal de Educação, Ciência e Tecnologia de Brasília, Campus Ceilândia, Brasília, DF, Brazil
| | | | - Elisabeth Ferroni Schwartz
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília, Brasília, Brazil.
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14
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Leite GGF, Ferreira BL, Tashima AK, Nishiduka ES, Cunha-Neto E, Brunialti MKC, Assuncao M, Azevedo LCP, Freitas F, van der Poll T, Scicluna BP, Salomão R. Combined Transcriptome and Proteome Leukocyte's Profiling Reveals Up-Regulated Module of Genes/Proteins Related to Low Density Neutrophils and Impaired Transcription and Translation Processes in Clinical Sepsis. Front Immunol 2021; 12:744799. [PMID: 34594344 PMCID: PMC8477441 DOI: 10.3389/fimmu.2021.744799] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/24/2021] [Indexed: 01/20/2023] Open
Abstract
Sepsis is a global health emergency, which is caused by various sources of infection that lead to changes in gene expression, protein-coding, and metabolism. Advancements in “omics” technologies have provided valuable tools to unravel the mechanisms involved in the pathogenesis of this disease. In this study, we performed shotgun mass spectrometry in peripheral blood mononuclear cells (PBMC) from septic patients (N=24) and healthy controls (N=9) and combined these results with two public microarray leukocytes datasets. Through combination of transcriptome and proteome profiling, we identified 170 co‐differentially expressed genes/proteins. Among these, 122 genes/proteins displayed the same expression trend. Ingenuity Pathway Analysis revealed pathways related to lymphocyte functions with decreased status, and defense processes that were predicted to be strongly increased. Protein-protein interaction network analyses revealed two densely connected regions, which mainly included down‐regulated genes/proteins that were related to the transcription of RNA, translation of proteins, and mitochondrial translation. Additionally, we identified one module comprising of up‐regulated genes/proteins, which were mainly related to low-density neutrophils (LDNs). LDNs were reported in sepsis and in COVID-19. Changes in gene expression level were validated using quantitative real-time PCR in PBMCs from patients with sepsis. To further support that the source of the upregulated module of genes/proteins found in our results were derived from LDNs, we identified an increase of this population by flow cytometry in PBMC samples obtained from the same cohort of septic patients included in the proteomic analysis. This study provides new insights into a reprioritization of biological functions in response to sepsis that involved a transcriptional and translational shutdown of genes/proteins, with exception of a set of genes/proteins related to LDNs and host‐defense system.
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Affiliation(s)
- Giuseppe Gianini Figueirêdo Leite
- Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, São Paulo, Brazil
| | - Bianca Lima Ferreira
- Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, São Paulo, Brazil
| | - Alexandre Keiji Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, São Paulo, Brazil
| | - Erika Sayuri Nishiduka
- Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, São Paulo, Brazil
| | - Edecio Cunha-Neto
- Laboratorio de Imunologia, Instituto do Coracao, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, Brazil
| | - Milena Karina Colo Brunialti
- Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, São Paulo, Brazil
| | - Murillo Assuncao
- Intensive Care Unit, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | | | - Flávio Freitas
- Intensive Care Unit, Hospital São Paulo, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Division of Infectious Diseases, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Brendon P Scicluna
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Department of Applied Biomedical Sciences, Faculty of Health Sciences, Mater Dei hospital, University of Malta, Msida, Malta
| | - Reinaldo Salomão
- Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, São Paulo, Brazil
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Han Q, Huang L, Li J, Wang Z, Gao H, Yang Z, Zhou Z, Liu Z. Neurotoxins in the venom gland of Calommata signata, a burrowing spider. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 40:100871. [PMID: 34315107 DOI: 10.1016/j.cbd.2021.100871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 05/06/2021] [Accepted: 06/18/2021] [Indexed: 11/18/2022]
Abstract
Calommata signata, a burrowing spider, represents a special type of predation mode in spiders, and its utilization of toxins is different from that of web-weaving spiders and wandering spiders. The existing researches on spider toxins are mainly focused on the web-weaving and wandering spiders, but little attention on that of the burrowing spiders. Through transcriptome sequencing of C. signata venom gland and the remaining part as the counterpart tissue, 25 putative neurotoxin precursors were identified. These most neurotoxins were novel because their low similarities with the known sequences except for that of over 50% similarities in four neuropeptide toxins. The 25 neuropeptide toxins were divided into five families according to the constitution of cysteines for the possible disulfide bonds and the similarities of the deduced amino acid sequences. Besides neuropeptide toxins, other potential toxins in the venom gland were also analyzed. Unlike web-weaving spiders and wandering spiders, only a few neurotoxin genes were significantly expressed in the venom gland of C. signata. In the non-peptide toxin genes, only CsTryp_SPc-1, CsPA2-1, CsVa5-2 and four PDI genes were abundantly expressed in the venom gland. The present study provided an improved understanding on the spider toxin diversity and useful information for the exploitation of spider toxins.
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Affiliation(s)
- Qianqian Han
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Lixin Huang
- Department of Applied Microbiology, Jiangsu Lixiahe District Institute of Agricultural Sciences/National Agricultural Experimental Station for Agricultural Microbiology, Yangzhou 225007, China
| | - Jingjing Li
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Zhaoying Wang
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Haoli Gao
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Zhiming Yang
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Zhangjin Zhou
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Zewen Liu
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China.
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Sahoo A, Swain SS, Behera A, Sahoo G, Mahapatra PK, Panda SK. Antimicrobial Peptides Derived From Insects Offer a Novel Therapeutic Option to Combat Biofilm: A Review. Front Microbiol 2021; 12:661195. [PMID: 34248873 PMCID: PMC8265172 DOI: 10.3389/fmicb.2021.661195] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/12/2021] [Indexed: 12/20/2022] Open
Abstract
Biofilms form a complex layer with defined structures, that attach on biotic or abiotic surfaces, are tough to eradicate and tend to cause some resistance against most antibiotics. Several studies confirmed that biofilm-producing bacteria exhibit higher resistance compared to the planktonic form of the same species. Antibiotic resistance factors are well understood in planktonic bacteria which is not so in case of biofilm producing forms. This may be due to the lack of available drugs with known resistance mechanisms for biofilms. Existing antibiotics cannot eradicate most biofilms, especially of ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species). Insects produce complex and diverse set of chemicals for survival and defense. Antimicrobial peptides (AMPs), produced by most insects, generally have a broad spectrum of activity and the potential to bypass the resistance mechanisms of classical antibiotics. Besides, AMPs may well act synergistically with classical antibiotics for a double-pronged attack on infections. Thus, AMPs could be promising alternatives to overcome medically important biofilms, decrease the possibility of acquired resistance and treatment of multidrug-resistant pathogens including ESKAPE. The present review focuses on insect-derived AMPs with special reference to anti-biofilm-based strategies. It covers the AMP composition, pathways and mechanisms of action, the formation of biofilms, impact of biofilms on human diseases, current strategies as well as therapeutic options to combat biofilm with antimicrobial peptides from insects. In addition, the review also illustrates the importance of bioinformatics tools and molecular docking studies to boost the importance of select bioactive peptides those can be developed as drugs, as well as suggestions for further basic and clinical research.
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Affiliation(s)
- Alaka Sahoo
- Department of Skin & VD, Institute of Medical Sciences, SUM Hospital, Siksha O Anusandhan University, Bhubaneswar, India
| | - Shasank Sekhar Swain
- Division of Microbiology & NCDs, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Ayusman Behera
- Department of Zoology, Maharaja Sriram Chandra Bhanja Deo University, Baripada, India
| | - Gunanidhi Sahoo
- Department of Zoology, Utkal University, Vani Vihar, Bhubaneswar, India
| | | | - Sujogya Kumar Panda
- Centre of Environment, Climate Change and Public Health, RUSA 2.0, Utkal University, Vani Vihar, Bhubaneswar, India
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17
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Mehta D, Ramesh A. Diversity and prevalence of ANTAR RNAs across actinobacteria. BMC Microbiol 2021; 21:159. [PMID: 34051745 PMCID: PMC8164766 DOI: 10.1186/s12866-021-02234-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 05/18/2021] [Indexed: 11/13/2022] Open
Abstract
Background Computational approaches are often used to predict regulatory RNAs in bacteria, but their success is limited to RNAs that are highly conserved across phyla, in sequence and structure. The ANTAR regulatory system consists of a family of RNAs (the ANTAR-target RNAs) that selectively recruit ANTAR proteins. This protein-RNA complex together regulates genes at the level of translation or transcriptional elongation. Despite the widespread distribution of ANTAR proteins in bacteria, their target RNAs haven’t been identified in certain bacterial phyla such as actinobacteria. Results Here, by using a computational search model that is tuned to actinobacterial genomes, we comprehensively identify ANTAR-target RNAs in actinobacteria. These RNA motifs lie in select transcripts, often overlapping with the ribosome binding site or start codon, to regulate translation. Transcripts harboring ANTAR-target RNAs majorly encode proteins involved in the transport and metabolism of cellular metabolites like sugars, amino acids and ions; or encode transcription factors that in turn regulate diverse genes. Conclusion In this report, we substantially diversify and expand the family of ANTAR RNAs across bacteria. These findings now provide a starting point to investigate the actinobacterial processes that are regulated by ANTAR. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02234-x.
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Affiliation(s)
- Dolly Mehta
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore, 560065, India.,SASTRA University, Tirumalaisamudram, Thanjavur, 613401, India
| | - Arati Ramesh
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore, 560065, India.
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