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Andersen HM, Tai HC, Rubakhin SS, Yau PM, Sweedler JV. A novel series of metazoan L/D peptide isomerases. J Biol Chem 2024; 300:107458. [PMID: 38857862 PMCID: PMC11277431 DOI: 10.1016/j.jbc.2024.107458] [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: 11/30/2023] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024] Open
Abstract
The function of endogenous cell-cell signaling peptides relies on their interactions with cognate receptors, which in turn are influenced by the peptides' structures, necessitating a comprehensive understanding of the suite of post-translational modifications of the peptide. Herein, we report the initial characterization of putative peptide isomerase enzymes extracted from R. norvegicus, A. californica, and B. taurus tissues. These enzymes are both tissue and substrate-specific across all three organisms. Notably, the lungs of the mammalian species, and the central nervous system of the mollusk displayed the highest isomerase activity among the examined tissues. In vitro enzymatic conversion was observed for several endogenous peptides, such as the tetrapeptide GFFD in A. californica, and mammalian neuropeptide FF in R. norvegicus and B. taurus. To understand their mode of action, we explored the effects of several inhibitors on these enzymes, which suggest common active site residues. While further characterization of these enzymes is required, the investigations emphasize a widespread and overlooked enzyme activity related to the creation of bioactive peptides.
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Affiliation(s)
- Harvey M Andersen
- Beckman Institute, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA; Department of Molecular and Integrative Physiology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA; Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Hua-Chia Tai
- Beckman Institute, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA; Department of Molecular and Integrative Physiology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Stanislav S Rubakhin
- Beckman Institute, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA; Department of Chemistry, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Peter M Yau
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan V Sweedler
- Beckman Institute, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA; Department of Molecular and Integrative Physiology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA; Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA; Department of Chemistry, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA.
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2
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Mast DH, Checco JW, Sweedler JV. Advancing d-amino acid-containing peptide discovery in the metazoan. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140553. [PMID: 33002629 DOI: 10.1016/j.bbapap.2020.140553] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/01/2020] [Accepted: 09/25/2020] [Indexed: 12/12/2022]
Abstract
The discovery of enzyme-derived d-amino acid-containing peptides (DAACPs) that have physiological importance in the metazoan challenges previous assumptions about the homochirality of animal proteins while simultaneously revealing new analytical challenges in the structural and functional characterization of peptides. Most known DAACPs have been identified though laborious activity-guided purification studies or by homology to previously identified DAACPs. Peptide characterization experiments are increasingly dominated by high throughput mass spectrometry-based peptidomics, with stereochemistry rarely considered due to the technical challenges of identifying l/d isomerization. This review discusses the prevalence of enzyme-derived DAACPs among animals and the physiological consequences of peptide isomerization. Also highlighted are the analytical methods that have been applied for structural characterization/discovery of DAACPs, including results of several recent studies using non-targeted discovery methods for revealing novel DAACPs, strongly suggesting that more DAACPs remain to be uncovered.
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Affiliation(s)
- David H Mast
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - James W Checco
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, United States.
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
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3
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Gu SX, Wang HF, Zhu YY, Chen FE. Natural Occurrence, Biological Functions, and Analysis of D-Amino Acids. PHARMACEUTICAL FRONTS 2020. [DOI: 10.1055/s-0040-1713820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
AbstractThis review covers the recent development on the natural occurrence, functional elucidations, and analysis of amino acids of the D (dextro) configuration. In the pharmaceutical field, amino acids are not only used directly as clinical drugs and nutriments, but also widely applied as starting materials, catalysts, or chiral ligands for the synthesis of active pharmaceutical ingredients. Earler belief hold that only L-amino acids exist in nature and D-amino acids were artificial products. However, increasing evidence indicates that D-amino acids are naturally occurring in living organisms including human beings, plants, and microorganisms, playing important roles in biological processes. While D-amino acids have similar physical and chemical characteristics with their respective L-enantiomers in an achiral measurement, the biological functions of D-amino acids are remarkably different from those of L-ones. With the rapid development of chiral analytical techniques for D-amino acids, studies on the existence, formation mechanisms, biological functions as well as relevant physiology and pathology of D-amino acids have achieved great progress; however, they are far from being sufficiently explored.
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Affiliation(s)
- Shuang-Xi Gu
- Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan, People's Republic of China
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan, People's Republic of China
| | - Hai-Feng Wang
- Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan, People's Republic of China
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan, People's Republic of China
| | - Yuan-Yuan Zhu
- School of Chemistry & Environmental Engineering, Wuhan Institute of Technology, Wuhan, People's Republic of China
| | - Fen-Er Chen
- Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan, People's Republic of China
- Department of Chemistry, Fudan University, Shanghai, People's Republic of China
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4
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Grishin DV, Zhdanov DD, Pokrovskaya MV, Sokolov NN. D-amino acids in nature, agriculture and biomedicine. ALL LIFE 2019. [DOI: 10.1080/21553769.2019.1622596] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
| | - D. D. Zhdanov
- Institute of Biomedical Chemistry, Moscow, Russia
- Peoples Friendship University of Russia, Moscow, Russia
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5
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Arthropod venoms: Biochemistry, ecology and evolution. Toxicon 2018; 158:84-103. [PMID: 30529476 DOI: 10.1016/j.toxicon.2018.11.433] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 11/20/2018] [Accepted: 11/26/2018] [Indexed: 12/17/2022]
Abstract
Comprising of over a million described species of highly diverse invertebrates, Arthropoda is amongst the most successful animal lineages to have colonized aerial, terrestrial, and aquatic domains. Venom, one of the many fascinating traits to have evolved in various members of this phylum, has underpinned their adaptation to diverse habitats. Over millions of years of evolution, arthropods have evolved ingenious ways of delivering venom in their targets for self-defence and predation. The morphological diversity of venom delivery apparatus in arthropods is astounding, and includes extensively modified pedipalps, tail (telson), mouth parts (hypostome), fangs, appendages (maxillulae), proboscis, ovipositor (stinger), and hair (urticating bristles). Recent investigations have also unravelled an astonishing venom biocomplexity with molecular scaffolds being recruited from a multitude of protein families. Venoms are a remarkable bioresource for discovering lead compounds in targeted therapeutics. Several components with prospective applications in the development of advanced lifesaving drugs and environment friendly bio-insecticides have been discovered from arthropod venoms. Despite these fascinating features, the composition, bioactivity, and molecular evolution of venom in several arthropod lineages remains largely understudied. This review highlights the prevalence of venom, its mode of toxic action, and the evolutionary dynamics of venom in Arthropoda, the most speciose phylum in the animal kingdom.
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Distinctive Roles of D-Amino Acids in the Homochiral World: Chirality of Amino Acids Modulates Mammalian Physiology and Pathology. Keio J Med 2018; 68:1-16. [PMID: 29794368 DOI: 10.2302/kjm.2018-0001-ir] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Living organisms enantioselectively employ L-amino acids as the molecular architecture of protein synthesized in the ribosome. Although L-amino acids are dominantly utilized in most biological processes, accumulating evidence points to the distinctive roles of D-amino acids in non-ribosomal physiology. Among the three domains of life, bacteria have the greatest capacity to produce a wide variety of D-amino acids. In contrast, archaea and eukaryotes are thought generally to synthesize only two kinds of D-amino acids: D-serine and D-aspartate. In mammals, D-serine is critical for neurotransmission as an endogenous coagonist of N-methyl D-aspartate receptors. Additionally, D-aspartate is associated with neurogenesis and endocrine systems. Furthermore, recognition of D-amino acids originating in bacteria is linked to systemic and mucosal innate immunity. Among the roles played by D-amino acids in human pathology, the dysfunction of neurotransmission mediated by D-serine is implicated in psychiatric and neurological disorders. Non-enzymatic conversion of L-aspartate or L-serine residues to their D-configurations is involved in age-associated protein degeneration. Moreover, the measurement of plasma or urinary D-/L-serine or D-/L-aspartate levels may have diagnostic or prognostic value in the treatment of kidney diseases. This review aims to summarize current understanding of D-amino-acid-associated biology with a major focus on mammalian physiology and pathology.
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Abstract
The search for new bioactive molecules that could be used in therapeutics is a major public health issue, particularly in the treatment of certain diseases such as cancer. In this context the exploration of the venom of animals (snakes, amphibians, cones, scorpions, insects...) that produce molecules of various structures and biological activities, is a very promising direction. Research in this area led to the discovery of neuropeptides, hormones, toxins, antimicrobial peptides and other extremely potent mediators. These are now used in many areas both in fundamental research and in translational research, respectively, to understand biochemical and physiological mechanisms, or to use as medical diagnostic tools and for therapeutic purposes. Pr. V. Erspamer is the first researcher to have shown, in the 1930s, that in addition to biogenic amines and alkaloids, granular glands from the skin of amphibians also produced huge amounts of peptides with various structures and biological activities. He also showed that these peptides had their counterparts, most often in the form of identical or similar peptides, in the central nervous system and the gastrointestinal tract of mammals. These observations are summarized in the form of a triangle concept of "brain-gut-skin" that states that any peptide found in a compartment should be present in the other two. In addition, abundance, ease of extraction and identification of peptides from amphibian skin make this model a means to search for their counterparts in mammals where they are present in minute quantities. This approach has two advantages: (i) at the fundamental level, the large peptide diversity, ubiquity and multiplicity of functions to which they participate, constitute a true chemical library to understand the mechanisms of recognition and signal transduction and study the physicochemical basic of the specificity; and (ii) in terms of applications, the relative simplicity of these peptides and the rise of the production techniques by chemical or recombinant synthesis offer an innovative potential for the development of molecules with pharmacological or therapeutic purposes.
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8
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Koehbach J, Gruber CW, Becker C, Kreil DP, Jilek A. MALDI TOF/TOF-Based Approach for the Identification of d- Amino Acids in Biologically Active Peptides and Proteins. J Proteome Res 2016; 15:1487-96. [PMID: 26985971 PMCID: PMC4861975 DOI: 10.1021/acs.jproteome.5b01067] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Several
biologically active peptides contain a d- amino
acid in a well-defined position, which is position 2 in all peptide
epimers isolated to date from vertebrates and also some from invertebrates.
The detection of such D- residues by standard analytical
techniques is challenging. In tandem mass spectrometric (MS) analysis,
although fragment masses are the same for all stereoisomers, peak
intensities are known to depend on chirality. Here, we observe that
the effect of a d- amino acid in the second N-terminal position
on the fragmentation pattern in matrix assisted laser desorption time-of-flight
spectrometry (MALDI-TOF/TOF MS) strongly depends on the peptide sequence.
Stereosensitive fragmentation (SF) is correlated to a neighborhood
effect, but the d- residue also exerts an overall effect
influencing distant bonds. In a fingerprint analysis, multiple peaks
can thus serve to identify the chirality of a sample in short time
and potentially high throughput. Problematic variations between individual
spots could be successfully suppressed by cospotting deuterated analogues
of the epimers. By identifying the [d-Leu2] isomer of the
predicted peptide GH-2 (gene derived bombininH) in skin secretions
of the toad Bombina orientalis, we
demonstrated the analytical power of SF-MALDI-TOF/TOF measurements.
In conclusion, SF-MALDI-TOF/TOF MS combines high sensitivity, versatility,
and the ability to complement other methods.
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Affiliation(s)
- Johannes Koehbach
- Centre for Physiology and Pharmacology, Medical University of Vienna , Schwarzspanierstraße 17, A-1090 Vienna, Austria.,School of Biomedical Sciences, The University of Queensland , Brisbane, QLD, 4072 Australia
| | - Christian W Gruber
- Centre for Physiology and Pharmacology, Medical University of Vienna , Schwarzspanierstraße 17, A-1090 Vienna, Austria
| | - Christian Becker
- Institute of Biological Chemistry, Department of Chemistry, University of Vienna , Währinger Straße 38, A-1090 Vienna, Austria
| | - David P Kreil
- Chair of Bioinformatics, University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
| | - Alexander Jilek
- Institute of Biological Chemistry, Department of Chemistry, University of Vienna , Währinger Straße 38, A-1090 Vienna, Austria.,Chair of Bioinformatics, University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
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9
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Ollivaux C, Soyez D, Toullec JY. Biogenesis of d
-amino acid containing peptides/proteins: where, when and how? J Pept Sci 2014; 20:595-612. [DOI: 10.1002/psc.2637] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 03/13/2014] [Accepted: 03/18/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Céline Ollivaux
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227; Integrative Biology of Marine Models, Station Biologique de Roscoff; CS 90074, F-29688 Roscoff cedex France
- CNRS, UMR 8227; Integrative Biology of Marine Models, Station Biologique de Roscoff; CS 90074, F-29688 Roscoff cedex France
| | - Daniel Soyez
- Sorbonne Universités, UPMC Univ Paris 06, ER3; Biogenèse des signaux peptidiques; 7 Quai Saint Bernard F-75251 Paris cedex 05 France
- CNRS, ER3; Biogenèse des signaux peptidiques; 7 Quai Saint Bernard F-75251 Paris cedex 05 France
| | - Jean-Yves Toullec
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7144; Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff; CS 90074, F-29688 Roscoff cedex France
- CNRS, UMR 7144; Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff; CS 90074, F-29688 Roscoff cedex France
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10
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‘Chiral compartmentation’ in metabolism: Enzyme stereo-specificity yielding evolutionary options. FEBS Lett 2013; 587:2790-7. [DOI: 10.1016/j.febslet.2013.05.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 05/04/2013] [Accepted: 05/06/2013] [Indexed: 10/26/2022]
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11
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Morishita F, Furukawa Y, Matsushima O. Molecular cloning of two distinct precursor genes of NdWFamide, a d-tryptophan-containing neuropeptide of the sea hare, Aplysia kurodai. Peptides 2012; 38:291-301. [PMID: 23000476 DOI: 10.1016/j.peptides.2012.08.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 08/22/2012] [Accepted: 08/22/2012] [Indexed: 10/27/2022]
Abstract
NdWFamide (NdWFa) is a D-tryptophan-containing cardioexcitatory neuropeptide in gastropod mollusks, such as Aplysia kurodai and Lymanea stagnalis. In this study, we have cloned two cDNA encoding distinct precursors for NdWFa from the abdominal ganglion of A. kurodai. One of the predicted precursor proteins consisted of 90 amino acids (NWF90), and the other consisted of 87 amino acids (NWF87). Both of the predicted precursor proteins have one NWFGKR sequence preceded by the N-terminal signal peptide. Sequential double staining by in situ hybridization (ISH) and immunostaining with anti-NdWFa antibody suggested that NdWFa-precursor and NdWFa peptide co-exist in neurons located in the right-upper quadrant region of the abdominal ganglion. In ISH, NWF90-specific signal and NWF87-specific one were found in different subsets of neurons in the abdominal ganglia of Aplysia. The expression level of NWF90 gene estimated by RT-PCR is much higher than that of NWF87 gene. These results suggest that NWF90 precursor is the major source of NdWFa in Aplysia ganglia.
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Affiliation(s)
- Fumihiro Morishita
- Department of Biological Science, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
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12
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Wong ESW, Morgenstern D, Mofiz E, Gombert S, Morris KM, Temple-Smith P, Renfree MB, Whittington CM, King GF, Warren WC, Papenfuss AT, Belov K. Proteomics and deep sequencing comparison of seasonally active venom glands in the platypus reveals novel venom peptides and distinct expression profiles. Mol Cell Proteomics 2012; 11:1354-64. [PMID: 22899769 DOI: 10.1074/mcp.m112.017491] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The platypus is a venomous monotreme. Male platypuses possess a spur on their hind legs that is connected to glands in the pelvic region. They produce venom only during the breeding season, presumably to fight off conspecifics. We have taken advantage of this unique seasonal production of venom to compare the transcriptomes of in- and out-of-season venom glands, in conjunction with proteomic analysis, to identify previously undiscovered venom genes. Comparison of the venom glands revealed distinct gene expression profiles that are consistent with changes in venom gland morphology and venom volumes in and out of the breeding season. Venom proteins were identified through shot-gun sequenced venom proteomes of three animals using RNA-seq-derived transcripts for peptide-spectral matching. 5,157 genes were expressed in the venom glands, 1,821 genes were up-regulated in the in-season gland, and 10 proteins were identified in the venom. New classes of platypus-venom proteins identified included antimicrobials, amide oxidase, serpin protease inhibitor, proteins associated with the mammalian stress response pathway, cytokines, and other immune molecules. Five putative toxins have only been identified in platypus venom: growth differentiation factor 15, nucleobindin-2, CD55, a CXC-chemokine, and corticotropin-releasing factor-binding protein. These novel venom proteins have potential biomedical and therapeutic applications and provide insights into venom evolution.
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Affiliation(s)
- Emily S W Wong
- Faculty of Veterinary Science, The University of Sydney, Camperdown, NSW 2006, Australia.
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13
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Detection of platypus-type l/d-peptide isomerase activity in aqueous extracts of papaya fruit. Biotechnol Lett 2012; 34:1659-65. [DOI: 10.1007/s10529-012-0941-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 04/25/2012] [Indexed: 10/28/2022]
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15
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Crone WJK, Leeper FJ, Truman AW. Identification and characterisation of the gene cluster for the anti-MRSA antibiotic bottromycin: expanding the biosynthetic diversity of ribosomal peptides. Chem Sci 2012. [DOI: 10.1039/c2sc21190d] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Gas chromatographic enantioseparation of derivatized α-amino acids on chiral stationary phases—Past and present. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:3122-40. [DOI: 10.1016/j.jchromb.2011.04.005] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 03/28/2011] [Accepted: 04/01/2011] [Indexed: 11/23/2022]
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17
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Gehmayr V, Mollay C, Reith L, Müller N, Jilek A. Tight binding of transition-state analogues to a peptidyl-aminoacyl-L/D-isomerase from frog skin. Chembiochem 2011; 12:1996-2000. [PMID: 21739559 PMCID: PMC3195878 DOI: 10.1002/cbic.201100203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Indexed: 11/30/2022]
Affiliation(s)
- Verena Gehmayr
- Institute of Organic Chemistry, Johannes Kepler University LinzAltenberger Strasse 69, 4040 Linz (Austria)
| | - Christa Mollay
- Institute of Molecular Biology, Austrian Academy of SciencesBillrothstrasse 11, 5020 Salzburg (Austria)
| | - Lorenz Reith
- Institute of Organic Chemistry, Johannes Kepler University LinzAltenberger Strasse 69, 4040 Linz (Austria)
| | - Norbert Müller
- Institute of Organic Chemistry, Johannes Kepler University LinzAltenberger Strasse 69, 4040 Linz (Austria)
| | - Alexander Jilek
- Chair of Bioinformatics, Department of Biotechnology, University of Natural Resources and Life SciencesMuthgasse 18, 1190 Vienna (Austria)
- Institute of Organic Chemistry, Johannes Kepler University LinzAltenberger Strasse 69, 4040 Linz (Austria)
- Institute of Molecular Biology, Austrian Academy of SciencesBillrothstrasse 11, 5020 Salzburg (Austria)
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18
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Wong ESW, Papenfuss AT, Whittington CM, Warren WC, Belov K. A limited role for gene duplications in the evolution of platypus venom. Mol Biol Evol 2011; 29:167-77. [PMID: 21816864 DOI: 10.1093/molbev/msr180] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Gene duplication followed by adaptive selection is believed to be the primary driver of venom evolution. However, to date, no studies have evaluated the importance of gene duplications for venom evolution using a genomic approach. The availability of a sequenced genome and a venom gland transcriptome for the enigmatic platypus provides a unique opportunity to explore the role that gene duplication plays in venom evolution. Here, we identify gene duplication events and correlate them with expressed transcripts in an in-season venom gland. Gene duplicates (1,508) were identified. These duplicated pairs (421), including genes that have undergone multiple rounds of gene duplications, were expressed in the venom gland. The majority of these genes are involved in metabolism and protein synthesis not toxin functions. Twelve secretory genes including serine proteases, metalloproteinases, and protease inhibitors likely to produce symptoms of envenomation such as vasodilation and pain were detected. Only 16 of 107 platypus genes with high similarity to known toxins evolved through gene duplication. Platypus venom C-type natriuretic peptides and nerve growth factor do not possess lineage-specific gene duplicates. Extensive duplications, believed to increase the potency of toxic content and promote toxin diversification, were not found. This is the first study to take a genome-wide approach in order to examine the impact of gene duplication on venom evolution. Our findings support the idea that adaptive selection acts on gene duplicates to drive the independent evolution and functional diversification of similar venom genes in venomous species. However, gene duplications alone do not explain the "venome" of the platypus. Other mechanisms, such as alternative splicing and mutation, may be important in venom innovation.
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Affiliation(s)
- Emily S W Wong
- Faculty of Veterinary Science, The University of Sydney, Sydney, New South Wales, Australia.
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19
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Experimental strategies for the analysis of D-amino acid containing peptides in crustaceans: a review. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:3102-7. [PMID: 21497143 DOI: 10.1016/j.jchromb.2011.03.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 03/10/2011] [Accepted: 03/17/2011] [Indexed: 11/23/2022]
Abstract
Detection of D-amino acids in natural peptides has been, and remains a challenging task, as peptidyl isomerization is a peculiar and subtle posttranslational modification that does not induce any change in primary sequence or in physicochemical properties of the molecule such as molecular mass or pI. Therefore, the presence of a D-amino acid residue in a peptide chain is generally transparent to classical methods of peptide analysis (electrophoresis, chromatography, mass spectrometry, molecular biology). In this article, we will review the various experimental strategies and analytical techniques, which have been used to characterize and to study D-amino acid containing peptides in crustaceans.
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20
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Jilek A, Mollay C, Lohner K, Kreil G. Substrate specificity of a peptidyl-aminoacyl-L/D-isomerase from frog skin. Amino Acids 2011; 42:1757-64. [PMID: 21424715 PMCID: PMC3325411 DOI: 10.1007/s00726-011-0890-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 03/09/2011] [Indexed: 12/14/2022]
Abstract
In the skin of fire-bellied toads (Bombina species), an aminoacyl-l/d-isomerase activity is present which catalyses the post-translational isomerization of the l- to the d-form of the second residue of its substrate peptides. Previously, this new type of enzyme was studied in some detail and genes potentially coding for similar polypeptides were found to exist in several vertebrate species including man. Here, we present our studies to the substrate specificity of this isomerase using fluorescence-labeled variants of the natural substrate bombinin H with different amino acids at positions 1, 2 or 3. Surprisingly, this enzyme has a rather low selectivity for residues at position 2 where the change of chirality at the alpha-carbon takes place. In contrast, a hydrophobic amino acid at position 1 and a small one at position 3 of the substrate are essential. Interestingly, some peptides containing a Phe at position 3 also were substrates. Furthermore, we investigated the role of the amino-terminus for substrate recognition. In view of the rather broad specificity of the frog isomerase, we made a databank search for potential substrates of such an enzyme. Indeed, numerous peptides of amphibia and mammals were found which fulfill the requirements determined in this study. Expression of isomerases with similar characteristics in other species can therefore be expected to catalyze the formation of peptides containing d-amino acids.
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Affiliation(s)
- Alexander Jilek
- Institute of Organic Chemistry, Johannes Kepler University Linz, Altenberger Str. 69, 4040, Linz, Austria.
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Koh JMS, Chow SJP, Crossett B, Kuchel PW. Mammalian peptide isomerase: platypus-type activity is present in mouse heart. Chem Biodivers 2010; 7:1603-11. [PMID: 20564672 DOI: 10.1002/cbdv.200900300] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Male platypus (Ornithorhynchus anatinus) venom has a peptidyl aminoacyl L/D-isomerase (hereafter called peptide isomerase) that converts the second amino acid residue in from the N-terminus from the L- to the D-form, and vice versa. A reversed-phase high-performance liquid chromatography (RP-HPLC) assay has been developed to monitor the interconversion using synthetic hexapeptides derived from defensin-like peptide-2 (DLP-2) and DLP-4 as substrates. It was hypothesised that animals other than the platypus would have peptide isomerase with the same substrate specificity. Accordingly, eight mouse tissues were tested and heart was shown to have the activity. This is notable for being the first evidence of a peptide isomerase being present in a higher mammal and heralds finding the activity in man.
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Affiliation(s)
- Jennifer M S Koh
- School of Molecular Biosciences, Building G08, University of Sydney, NSW 2006, Australia
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Abstract
The monotremes (the echidnas and the platypus) display both mammalian and reptilian features. Male monotremes have a bilateral crural gland that is connected via a duct to a spur on each hind limb. Male echidnas appear not to use their spurs as weapons in aggressive acts, but the crural system may have a role in reproductive behaviour because it appears only to be active during the breeding season. The secretions produced by the echidna’s crural gland have not hitherto been biochemically or pharmacologically characterised. We used reverse-phase high-performance liquid chromatography (RP-HPLC) to separate the components of echidna venom and compared the chromatograms with those from platypus venom. The echidna venom appears to contain fewer proteins and peptides than platypus venom; however, it appears to have defensin-like peptides that behave similarly on RP-HPLC to those in platypus venom. Like platypus venom, echidna venom has peptidyl aminoacyl l/d-peptide isomerase activity. An RP-HPLC-based assay showed that the second amino acid residue, of a probe synthetic hexapeptide, was converted into the d-form, when incubated with echidna venom.
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Nandi N. Chiral discrimination in the confined environment of biological nanospace: reactions and interactions involving amino acids and peptides. INT REV PHYS CHEM 2009. [DOI: 10.1080/01442350902999682] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Whittington CM, Koh JM, Warren WC, Papenfuss AT, Torres AM, Kuchel PW, Belov K. Understanding and utilising mammalian venom via a platypus venom transcriptome. J Proteomics 2009; 72:155-64. [DOI: 10.1016/j.jprot.2008.12.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Accepted: 12/11/2008] [Indexed: 01/10/2023]
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Abstract
An anatomical feature of the platypus (Ornithorhynchus anatinus) that is seen in only one other mammal, the echidna, is that the male has a crural glandular system that produces venom that is used for defence and territorial–breeding functions; whether the echidna is similarly venomous is not yet established. Platypus venom contains many novel proteins and peptides that are different from those in reptilian venom. It also causes pain and symptoms that are not experienced by any other kind of envenomation. Five types of proteins and peptides have been isolated and identified from platypus venom, namely: defensin-like peptides (DLPs); Ornithorhynchus venom C-type natriuretic peptides (OvCNPs); Ornithorhynchus nerve growth factor; hyaluronidase; and l-to-d-peptide isomerase. The structures of DLPs and OvCNPs have already been studied and they are very similar to β-defensin-12 and mammalian C-type natriuretic peptides, respectively. A special mammalian l-to-d-peptide isomerase that is responsible for interconverting the l- and d-peptide isomers is also found in platypus venom. Isomerase activity has recently been discovered in platypus tissues other than the venom gland. It is possible that similar kinds of enzymes might exist in other mammals and play important, as yet unknown, biological roles. Considering the fact that some animal venoms have already been widely used in pharmaceutical applications, research into platypus venom may lead to the discovery of new molecules and potent drugs that are useful biomedical tools.
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Zangger K, Gößler R, Khatai L, Lohner K, Jilek A. Structures of the glycine-rich diastereomeric peptides bombinin H2 and H4. Toxicon 2008; 52:246-54. [DOI: 10.1016/j.toxicon.2008.05.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Revised: 04/30/2008] [Accepted: 05/01/2008] [Indexed: 11/26/2022]
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Whittington CM, Papenfuss AT, Kuchel PW, Belov K. Expression patterns of platypus defensin and related venom genes across a range of tissue types reveal the possibility of broader functions for OvDLPs than previously suspected. Toxicon 2008; 52:559-65. [PMID: 18662710 DOI: 10.1016/j.toxicon.2008.07.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Revised: 06/28/2008] [Accepted: 07/01/2008] [Indexed: 11/30/2022]
Abstract
The platypus, as an egg-laying mammal, displays an unusual mixture of reptilian and mammalian characteristics. It is also venomous, and further investigations into its little-studied venom may lead to the development of novel pharmaceuticals and drug targets and provide insights into the origins of mammalian venom. Here we investigate the expression patterns of antimicrobial genes called defensins, and also the venom peptides called defensin-like peptides (OvDLPs). We show, in the first expression study on any platypus venom gene, that the OvDLPs are expressed in a greater range of tissues than would be expected for genes with specific venom function, and thus that they may have a wider role than previously suspected.
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Affiliation(s)
- Camilla M Whittington
- Faculty of Veterinary Science, RMC Gunn B19, University of Sydney, NSW 2006, Australia
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Ewing MA, Wang J, Sheeley SA, Sweedler JV. Detecting D-amino acid-containing neuropeptides using selective enzymatic digestion. Anal Chem 2008; 80:2874-80. [PMID: 18341354 DOI: 10.1021/ac7025173] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Neuropeptides, gene products that undergo extensive post-translational modification (PTM), are frequently characterized using mass spectrometry (MS). One PTM in particular, the conversion of an L-amino acid to a D-amino acid, has no associated mass shift. Therefore, this PTM is difficult to evaluate using MS alone, especially in complex peptide mixtures. Here, enzymatic digestion using microsomal alanyl aminopeptidase is combined with MS characterization. This enzyme selectively degrades peptides lacking a D-amino acid in the second position from the N-terminus. By comparing a sample before and after digestion, D-amino acid-containing peptides (DAACPs) present in small quantities in a complex mixture can be identified, even among much larger quantities of other non-DAACPs. Protocols that use microsomal alanyl aminopeptidase as a discovery-enabling agent are described and validated by identifying a known DAACP from the Aplysia californica abdominal ganglion.
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Affiliation(s)
- Michael A Ewing
- Department of Chemistry and the Beckman Institute, University of Illinois, Urbana, Illinois 61801, USA
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Bansal PS, Torres AM, Crossett B, Wong KKY, Koh JMS, Geraghty DP, Vandenberg JI, Kuchel PW. Substrate specificity of platypus venom L-to-D-peptide isomerase. J Biol Chem 2007; 283:8969-75. [PMID: 18158286 DOI: 10.1074/jbc.m709762200] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The L-to-D-peptide isomerase from the venom of the platypus (Ornithorhyncus anatinus) is the first such enzyme to be reported for a mammal. In delineating its catalytic mechanism and broader roles in the animal, its substrate specificity was explored. We used N-terminal segments of defensin-like peptides DLP-2 and DLP-4 and natriuretic peptide OvCNP from the venom as substrates. The DLP analogues IMFsrs and ImFsrs (srs is a solubilizing chain; lowercase letters denote D-amino acid) were effective substrates for the isomerase; it appears to recognize the N-terminal tripeptide sequence Ile-Xaa-Phe-. A suite of 26 mutants of these hexapeptides was synthesized by replacing the second residue (Met) with another amino acid, viz. Ala, alpha-aminobutyric acid, Ile, Leu, Lys, norleucine, Phe, Tyr, and Val. It was shown that mutant peptides incorporating norleucine and Phe are substrates and exhibit L- or D-amino acid isomerization, but mutant peptides that contain residues with shorter, beta-branched or long side chains with polar terminal groups, viz. Ala, alpha-aminobutyric acid, Ile, Val, Leu, Lys, and Tyr, respectively, are not substrates. It was demonstrated that at least three N-terminal amino acid residues are absolutely essential for L-to-D-isomerization; furthermore, the third amino acid must be a Phe residue. None of the hexapeptides based on LLH, the first three residues of OvCNP, were substrates. A consistent 2-base mechanism is proposed for the isomerization; abstraction of a proton by 1 base is concomitant with delivery of a proton by the conjugate acid of a second base.
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Affiliation(s)
- Paramjit S Bansal
- School of Molecular and Microbial Biosciences, University of Sydney, New South Wales 2006, Australia
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