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Medina-Santos R, Fernandes Costa TG, Silva de Assis TC, Kalapothakis Y, de Almeida Lima S, do Carmo AO, Gonzalez-Kozlova EE, Kalapothakis E, Chávez-Olórtegui C, Guerra-Duarte C. Analysis of NGS data from Peruvian Loxosceles laeta spider venom gland reveals toxin diversity. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 43:101017. [PMID: 35932519 DOI: 10.1016/j.cbd.2022.101017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/12/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Accidents involving spiders from the genus Loxosceles cause medical emergencies in several countries of South America. The species Loxosceles laeta is ubiquitously present in Peru and is responsible for severe accidents in this country. To further characterize L. laeta venom components and to unveil possible variations in the Peruvian population, we provide an overview of the toxins-related transcripts present in the venom gland of Peruvian L. laeta. A dataset from a cDNA library previously sequenced by MiSeq sequencer (Illumina) was re-analyzed and the obtained data was compared with available sequences from Loxosceles toxins. Phospholipase-D represent the majority (69,28 %) of the transcripts related to venom toxins, followed by metalloproteases (20,72 %), sicaritoxins (6,03 %), serine-proteases (2,28 %), hyaluronidases (1,80 %) and Translationally Controlled Tumor Protein (TCTP) (0,56 %). New sequences of phospholipases D,sicaritoxins, hyaluronidase, TCTP and serine proteinases were described. Differences between the here-described toxin sequences and others, previously identified in venom glands from other spiders, were visualized upon sequence alignments. In addition, an in vitro hyaluronidase activity assay was also performed to complement comparisons between Peruvian and Brazilian L. laeta venom enzymatic activities, revealing a superior activity in the venom from Brazilian specimens. These new data provide a molecular basis that can help to explain the difference in toxicity among L. laeta venoms from different countries in South America.
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Affiliation(s)
- Raíssa Medina-Santos
- Biochemistry and Immunology Department, Federal University of Minas Gerais, Brazil; Genetic, Ecology and Evolution Department, Federal University of Minas Gerais, Brazil
| | | | | | - Yan Kalapothakis
- Genetic, Ecology and Evolution Department, Federal University of Minas Gerais, Brazil
| | | | | | - Edgar E Gonzalez-Kozlova
- Department of Genetics and Genomic Sciences, Icahn School for Data Science and Genomic Technology, New York, United States of America
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2
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Carugo O. Survey of the Intermolecular Disulfide Bonds Observed in Protein Crystal Structures Deposited in the Protein Data Bank. LIFE (BASEL, SWITZERLAND) 2022; 12:life12070986. [PMID: 35888076 PMCID: PMC9323673 DOI: 10.3390/life12070986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 11/29/2022]
Abstract
About 5% of the disulfide bonds (DBs) observed in the Protein Data Bank bridge two protein chains. Several of their features were comprehensively analyzed, resulting in a structural atlas of the intermolecular DBs. The analysis was performed on a very large set of data extracted from the Protein Data Bank, according to the RaSPDB procedure. It was observed that the two chains tend to have different sequences and belong to the same structural class. Intermolecular DBs tend to be more solvent accessible and less distorted from the most stable conformation than intermolecular DBs while showing similar B-factors. They tend to occur in beta strands and in mainly-beta structures. These and other data should prove useful in protein modelling and design.
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Affiliation(s)
- Oliviero Carugo
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy;
- Italy & Max Perutz Labs, Department of Structural and Computational Biology, University of Vienna, 1010 Wien, Austria
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Diniz MRV, Paiva ALB, Guerra-Duarte C, Nishiyama MY, Mudadu MA, de Oliveira U, Borges MH, Yates JR, Junqueira-de-Azevedo IDL. An overview of Phoneutria nigriventer spider venom using combined transcriptomic and proteomic approaches. PLoS One 2018; 13:e0200628. [PMID: 30067761 PMCID: PMC6070231 DOI: 10.1371/journal.pone.0200628] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 06/29/2018] [Indexed: 01/23/2023] Open
Abstract
Phoneutria nigriventer is one of the largest existing true spiders and one of the few considered medically relevant. Its venom contains several neurotoxic peptides that act on different ion channels and chemical receptors of vertebrates and invertebrates. Some of these venom toxins have been shown as promising models for pharmaceutical or biotechnological use. However, the large diversity and the predominance of low molecular weight toxins in this venom have hampered the identification and deep investigation of the less abundant toxins and the proteins with high molecular weight. Here, we combined conventional and next-generation cDNA sequencing with Multidimensional Protein Identification Technology (MudPIT), to obtain an in-depth panorama of the composition of P. nigriventer spider venom. The results from these three approaches showed that cysteine-rich peptide toxins are the most abundant components in this venom and most of them contain the Inhibitor Cysteine Knot (ICK) structural motif. Ninety-eight sequences corresponding to cysteine-rich peptide toxins were identified by the three methodologies and many of them were considered as putative novel toxins, due to the low similarity to previously described toxins. Furthermore, using next-generation sequencing we identified families of several other classes of toxins, including CAPs (Cysteine Rich Secretory Protein-CRiSP, antigen 5 and Pathogenesis-Related 1-PR-1), serine proteinases, TCTPs (translationally controlled tumor proteins), proteinase inhibitors, metalloproteinases and hyaluronidases, which have been poorly described for this venom. This study provides an overview of the molecular diversity of P. nigriventer venom, revealing several novel components and providing a better basis to understand its toxicity and pharmacological activities.
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MESH Headings
- Amino Acid Sequence
- Animals
- Biomarkers, Tumor/chemistry
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/metabolism
- High-Throughput Nucleotide Sequencing
- Membrane Glycoproteins/chemistry
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/metabolism
- Peptides/metabolism
- Proteomics
- Sequence Alignment
- Sequence Analysis, DNA
- Spider Venoms/metabolism
- Spiders/genetics
- Spiders/metabolism
- Toxins, Biological/genetics
- Toxins, Biological/metabolism
- Transcriptome
- Tumor Protein, Translationally-Controlled 1
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Affiliation(s)
- Marcelo R. V. Diniz
- Laboratório de Toxinologia Molecular, Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Ana L. B. Paiva
- Laboratório de Toxinologia Molecular, Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Clara Guerra-Duarte
- Laboratório de Toxinologia Molecular, Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Milton Y. Nishiyama
- Laboratório Especial de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, SP, Brazil
| | | | - Ursula de Oliveira
- Laboratório Especial de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, SP, Brazil
| | - Márcia H. Borges
- Laboratório de Toxinologia Molecular, Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - John R. Yates
- Department of Chemical Physiology and Molecular and Cellular Neurobiology, The Scripps Research Institute, La Jolla, California, United States of America
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4
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Porto WF, Miranda VJ, Pinto MFS, Dohms SM, Franco OL. High-performance computational analysis and peptide screening from databases of cyclotides from poaceae. Biopolymers 2017; 106:109-18. [PMID: 26572696 DOI: 10.1002/bip.22771] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/21/2015] [Accepted: 11/09/2015] [Indexed: 12/22/2022]
Abstract
Cyclotides are a family of head-to-tail cyclized peptides containing three conserved disulfide bonds, in a structural scaffold also known as a cyclic cysteine knot. Due to the high degree of cysteine conservation, novel members from this peptide family can be identified in protein databases through a search through regular expression (REGEX). In this work, six novel cyclotide-like precursors from the Poaceae were identified from NCBI's non-redundant protein database by the use of REGEX. Two out of six sequences (named Zea mays L and M) showed an Asp residue in the C-terminal, which indicated that they could be cyclic. Gene expression in maize tissues was investigated, showing that the previously described cyclotide-like Z. mays J is expressed in the roots. According to molecular dynamics, the structure of Z. mays J seems to be stable, despite the putative absence of cyclization. As regards cyclotide evolution, it was hypothesized that this is an outcome from convergent evolution and/or horizontal gene transfer. The results showed that peptide screening from databases should be performed periodically in order to include novel sequences, which are deposited as the databases grow. Indeed, the advances in computational and experimental methods will together help to answer key questions and reach new horizons in defense-related peptide identification.
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Affiliation(s)
- William F Porto
- Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia Universidade Católica De Brasília, Brasília-DF, Brazil
| | - Vivian J Miranda
- Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia Universidade Católica De Brasília, Brasília-DF, Brazil
| | - Michelle F S Pinto
- Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia Universidade Católica De Brasília, Brasília-DF, Brazil
| | - Stephan M Dohms
- Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia Universidade Católica De Brasília, Brasília-DF, Brazil
| | - Octavio L Franco
- Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia Universidade Católica De Brasília, Brasília-DF, Brazil.,S-Inova Biotech, Pos Graduação em Biotecnologia, Universidade Catolica Dom Bosco, Campo Grande MS, Brazil
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Synthetic Cystine-Knot Miniproteins - Valuable Scaffolds for Polypeptide Engineering. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 917:121-44. [PMID: 27236555 DOI: 10.1007/978-3-319-32805-8_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Peptides with the cystine-knot architecture, often termed knottins, are promising scaffolds for biomolecular engineering. These unique molecules combine diverse bioactivities with excellent structural, thermal, and proteolytical stability. Being different in the composition and structure of their amino acid backbone, knottins share the same core element, namely cystine knot, which is built by six cysteine residues forming three disulfides upon oxidative folding. This motif ensures a notably rigid framework that highly tolerates both rational and combinatorial changes in the primary structure. Being accessible through recombinant production and total chemical synthesis, cystine-knot miniproteins can be endowed with novel bioactivities by variation of surface-exposed loops and incorporation of non-natural elements within their non-conserved regions towards the generation of tailor-made peptidic compounds. In this chapter the topology of cystine-knot peptides, their synthesis and applications for diagnostics and therapy is discussed.
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Gillet FX, Cattoni DI, Petiot-Bécard S, Delalande F, Poignavent V, Brizard JP, Bessin Y, Dorsselaer AV, Declerck N, Sanglier-Cianférani S, Brugidou C, Vignols F. The RYMV-Encoded Viral Suppressor of RNA Silencing P1 Is a Zinc-Binding Protein with Redox-Dependent Flexibility. J Mol Biol 2013; 425:2423-35. [DOI: 10.1016/j.jmb.2013.03.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 03/14/2013] [Accepted: 03/18/2013] [Indexed: 10/27/2022]
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Parachin NS, Mulder KC, Viana AAB, Dias SC, Franco OL. Expression systems for heterologous production of antimicrobial peptides. Peptides 2012; 38:446-56. [PMID: 23022589 DOI: 10.1016/j.peptides.2012.09.020] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 09/16/2012] [Accepted: 09/16/2012] [Indexed: 12/21/2022]
Abstract
Antimicrobial peptides (AMPs) consist of molecules that act on the defense systems of numerous organisms toward multiple pathogens such as bacteria, fungi, parasites and viruses. These compounds have become extremely significant due to the increasing resistance of microorganisms to common antibiotics. However, the low quantity of peptides obtained from direct purification is, to date, still a remarkable bottleneck for scientific and industrial research development. Therefore, this review describes the main heterologous systems currently used for AMP production, including bacteria, fungi and plants, and also the related strategies for reaching greater functional peptide production. The main difficulties of each system are also described in order to provide some directions for AMP production. In summary, data revised here indicate that large-scale production of AMPs can be obtained using biotechnological tools, and the products may be applied in the pharmaceutical industry as well as in agribusiness.
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Affiliation(s)
- Nádia Skorupa Parachin
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
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8
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Chemical synthesis, backbone cyclization and oxidative folding of cystine-knot peptides: promising scaffolds for applications in drug design. Molecules 2012; 17:12533-52. [PMID: 23095896 PMCID: PMC6268209 DOI: 10.3390/molecules171112533] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 09/19/2012] [Accepted: 10/22/2012] [Indexed: 02/03/2023] Open
Abstract
Cystine-knot peptides display exceptional structural, thermal, and biological stability. Their eponymous motif consists of six cysteine residues that form three disulfide bonds, resulting in a notably rigid structural core. Since they highly tolerate either rational or combinatorial changes in their primary structure, cystine knots are considered to be promising frameworks for the development of peptide-based pharmaceuticals. Despite their relatively small size (two to three dozens amino acid residues), the chemical synthesis route is challenging since it involves critical steps such as head-to-tail cyclization and oxidative folding towards the respective bioactive isomer. Herein we describe the topology of cystine-knot peptides, their synthetic availability and briefly discuss potential applications of engineered variants in diagnostics and therapy.
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Clement H, Olvera A, Rodríguez M, Zamudio F, Palomares LA, Possani LD, Odell GV, Alagón A, Sánchez-López R. Identification, cDNA cloning and heterologous expression of a hyaluronidase from the tarantula Brachypelma vagans venom. Toxicon 2012; 60:1223-7. [PMID: 22982117 DOI: 10.1016/j.toxicon.2012.08.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 08/21/2012] [Accepted: 08/29/2012] [Indexed: 12/22/2022]
Abstract
Hyaluronidases (Hyal) present in the venom of poisonous animals have been considered as "spreading factors" that facilitate a fast penetration of the venom in the prey. We have found that hyaluronidase from the tarantula Brachypelma vagans venom (BvHyal) displays a substrate-specific Hyal activity against hyaluronan. By using a combined strategy based on peptide sequencing and RT-PCR, we have cloned a BvHyal cDNA. Active recombinant BvHyal was efficiently expressed in a baculovirus system in insect cell.
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Affiliation(s)
- Herlinda Clement
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mor. 62250, Mexico
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10
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Pinto MFS, Almeida RG, Porto WF, Fensterseifer ICM, Lima LA, Dias SC, Franco OL. Cyclotides. J Evid Based Complementary Altern Med 2011. [DOI: 10.1177/2156587211428077] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In recent years, a number of peptides containing a cyclic structural fold have been described. Among them, the cyclotides family was widely reported in different plant tissues, being composed of small cyclic peptides containing 6 conserved cysteine residues connected by disulfide bonds and forming a cysteine-binding cyclic structure known as a cyclic cysteine knot. This structural scaffold is responsible for an enhanced structural stability against chemical, thermal, and proteolytic degradation. Because of the observed stability and multifunctionality, including insecticidal, antimicrobial, and anti-HIV (human immunodeficiency virus) action, much effort has gone into trying to elucidate the structural-function relations of cyclotide compounds. This review focuses on the novelties involving gene structure, precursor formation and processing, and protein folding of the cyclotide family, shedding some light on molecular mechanisms of cyclotide production. Because cyclotides are clear targets for drug development and also biotechnology applications, their chemical synthesis, heterologous systems production, and protein grafting are also addressed.
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