1
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Yussif BM, Checco JW. Evaluation of endogenous peptide stereochemistry using liquid chromatography-mass spectrometry-based spiking experiments. Methods Enzymol 2022; 663:205-234. [DOI: 10.1016/bs.mie.2021.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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2
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Yamagishi H, Sato H, Kawamura I. Vibrational circular dichroism of D-amino acid-containing peptide NdWFamide in the crystal form. Chirality 2021; 33:652-659. [PMID: 34313360 DOI: 10.1002/chir.23343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/02/2021] [Accepted: 07/08/2021] [Indexed: 01/31/2023]
Abstract
Microcrystals of l-Asn-d-Trp-l-Phe-NH2 (NdWFamide), a tripeptide derived from Aplysia kurodai that exhibits invertebrate cardiac activity, were evaluated by vibrational circular dichroism (VCD). The chirality of the tryptophan residue at the second position in NdWFamide was associated with the conformation and biological characteristics. The VCD spectrum of NdWFamide was a mirror image of its enantiomer; however, it was significantly different from that of its diastereomer, NWFamide, which is its precursor. The obtained VCD signals of NdWFamide were in good agreement with the VCD signals that were calculated based on the optimized aggregates of NdWFamide, which formed a helical-like backbone conformation. The evaluation of the VCD results revealed the conformation of NdWFamide in the crystalline state and succeeded in distinguishing its stereoisomers. Therefore, this study demonstrates VCD as a useful method for the structural analysis of naturally occurring d-amino acid-containing peptides.
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Affiliation(s)
- Hiroki Yamagishi
- Graduate School of Engineering Science, Yokohama National University, Yokohama, Japan
| | - Hisako Sato
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
| | - Izuru Kawamura
- Graduate School of Engineering Science, Yokohama National University, Yokohama, Japan
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3
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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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4
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Separation of D-amino acid-containing peptide phenylseptin using 3,3'-phenyl-1,1'-binaphthyl-18-crown-6-ether columns. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140429. [PMID: 32298805 DOI: 10.1016/j.bbapap.2020.140429] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/05/2020] [Accepted: 04/09/2020] [Indexed: 12/19/2022]
Abstract
Several D-amino acid-containing peptides (DAACPs) with antimicrobial, cardio-excitatory, or neuronal activities have been found in several species. Here, we demonstrated the chiral separation of the antimicrobial peptide diastereomers, D-phenylseptin and L-phenylseptin using (S) and (R) 3,3'-phenyl-1,1'-binaphthyl-18-crown-6-ether columns (CR-I (+) and CR-I (-), respectively) and also investigated the underlying mechanism. First, using D-amino acid-containing tripeptide Phe-Phe-Phe-OH, we found that CR-I (+) could be used to recognize diastereomeric tripeptides containing an L-amino acid as the first residue. On the contrary, CR-I (-) enabled separation of a series of diastereomers with D-amino acid as the first residue. Therefore, we achieved separation of the stereoisomers using the chiral columns depending on the position of the D- amino acid in the peptide and demonstrated the orthogonality of separations of the chiral columns. Then, using CR-I (+), we separated amphibian antimicrobial peptide diastereomers, L- and D-phenylseptin, which have the sequences, L-Phe-L-Phe-L-Phe and L-Phe-D-Phe-L-Phe at their N-termini, respectively. In order to understand the host-guest interactions, we performed molecular dynamics simulations for L-Phe-L-Phe-L-Phe tripeptide-CR-I molecule complex systems. Three hydrogen bonds between the N-terminal amine group -NH3+ and the crown ether oxygens were the dominant interactions. The hydrophobic interactions between phenyl-rings in the chiral selector unit of CR-I (+) and the side chains of 2nd and 3rd residues of the peptide also contributed to the affinity. Our results show that the CR-I (+)-column can be applied for the separation of endogenous DAACPs generated by the post-translational modification.
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5
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Mast DH, Checco JW, Sweedler JV. Differential Post-Translational Amino Acid Isomerization Found among Neuropeptides in Aplysia californica. ACS Chem Biol 2020; 15:272-281. [PMID: 31877009 DOI: 10.1021/acschembio.9b00910] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
d-Amino acid-containing peptides (DAACPs) make up a class of post-translationally modified peptides in animals that play important roles as cell-to-cell signaling molecules. Despite the functional importance of l- to d-residue isomerization, little is known about its prevalence, mostly due to difficulties associated with detecting differences in peptide stereochemistry. Prior efforts to discover DAACPs have been largely focused on pursuing peptides based on homology to known DAACPs or DAACP-encoding precursors. Here, we used a combination of enzymatic screening, mass spectrometry, and chromatographic analysis to identify novel DAACPs in the central nervous system (CNS) of Aplysia californica. We identified five new DAACPs from the pleurin precursor and three DAACPs from previously uncharacterized proteins. In addition, two peptides from the pleurin precursor, Plrn2 and Plrn3, exist as DAACPs with the d-residue found at position 2 or 3. These differentially modified forms of Plrn2 and Plrn3 are located in specific regions of the animal's CNS. Plrn2 and Plrn3 appear to be the first animal DAACPs in which the d-residue is found at more than one position, and this suggests that l- to d-residue isomerization may be a more variable/dynamic modification than previously thought. Overall, this study demonstrates the utility of nontargeted DAACP discovery approaches for identifying new DAACPs and demonstrates that isomerization is prevalent throughout the CNS of A. californica.
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Affiliation(s)
- David H. Mast
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - James W. Checco
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V. Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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6
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Fujii N, Takata T, Fujii N, Aki K, Sakaue H. D-Amino acids in protein: The mirror of life as a molecular index of aging. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018. [DOI: 10.1016/j.bbapap.2018.03.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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7
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Ha S, Kim I, Takata T, Kinouchi T, Isoyama M, Suzuki M, Fujii N. Identification of ᴅ-amino acid-containing peptides in human serum. PLoS One 2017; 12:e0189972. [PMID: 29253022 PMCID: PMC5734745 DOI: 10.1371/journal.pone.0189972] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/05/2017] [Indexed: 12/12/2022] Open
Abstract
Biologically uncommon d-aspartate (d-Asp) residues have been shown to accumulate in proteins associated with age-related human disorders, such as cataract and Alzheimer disease. Such d-Asp-containing proteins are unlikely to be broken down completely because metabolic enzymes recognize only proteins or peptides composed exclusively of l-amino acids. Therefore, undigested d-Asp-containing peptides may exist in blood and, if detectable, may be a useful biomarker for associated diseases. In this study, we investigated d-amino acid-containing peptides in adult human serum by a qualitative d-amino acid analysis based on a diastereomer method and LC-MS/MS method. As a result, two d-Asp-containing peptides were detected in serum, both derived from the fibrinogen β-chain, a glycoprotein that helps in the formation of blood clots. One of the peptides was fibrinopeptide B, which prevents fibrinogen from forming polymers of fibrin, and the other was same peptide with C-terminal Arginine missing. To our knowledge, this is the first report of the presence of d-amino acid-containing peptides in serum and the approach described will provide a new direction on the serum proteome and fragmentome.
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Affiliation(s)
- Seongmin Ha
- Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Ingu Kim
- Research Reactor Institute, Kyoto University, Osaka, Japan
| | - Takumi Takata
- Research Reactor Institute, Kyoto University, Osaka, Japan
| | - Tadatoshi Kinouchi
- Graduate School of Science, Kyoto University, Kyoto, Japan
- Research Reactor Institute, Kyoto University, Osaka, Japan
| | | | - Minoru Suzuki
- Research Reactor Institute, Kyoto University, Osaka, Japan
| | - Noriko Fujii
- Research Reactor Institute, Kyoto University, Osaka, Japan
- * E-mail:
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8
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Fouque KJD, Garabedian A, Porter J, Baird M, Pang X, Williams TD, Li L, Shvartsburg A, Fernandez-Lima F. Fast and Effective Ion Mobility-Mass Spectrometry Separation of d-Amino-Acid-Containing Peptides. Anal Chem 2017; 89:11787-11794. [PMID: 28982001 PMCID: PMC5677546 DOI: 10.1021/acs.analchem.7b03401] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Despite often minute concentrations in vivo, d-amino acid containing peptides (DAACPs) are crucial to many life processes. Standard proteomics protocols fail to detect them as d/l substitutions do not affect the peptide parent and fragment masses. The differences in fragment yields are often limited, obstructing the investigations of important but low abundance epimers in isomeric mixtures. Separation of d/l-peptides using ion mobility spectrometry (IMS) was impeded by small collision cross section differences (commonly ∼1%). Here, broad baseline separation of DAACPs with up to ∼30 residues employing trapped IMS with resolving power up to ∼340, followed by time-of-flight mass spectrometry is demonstrated. The d/l-pairs coeluting in one charge state were resolved in another, and epimers merged as protonated species were resolved upon metalation, effectively turning the charge state and cationization mode into extra separation dimensions. Linear quantification down to 0.25% proved the utility of high resolution IMS-MS for real samples with large interisomeric dynamic range. Very close relative mobilities found for DAACP pairs using traveling-wave IMS (TWIMS) with different ion sources and faster IMS separations showed the transferability of results across IMS platforms. Fragmentation of epimers can enhance their identification and further improve detection and quantification limits, and we demonstrate the advantages of online mobility separated collision-induced dissociation (CID) followed by high resolution mass spectrometry (TIMS-CID-MS) for epimer analysis.
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Alyssa Garabedian
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Jacob Porter
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Matthew Baird
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Xueqin Pang
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Todd D. Williams
- Mass Spectrometry Laboratory, University of Kansas, Lawrence, KS 66045, USA
| | - Lingjun Li
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53705, USA
| | | | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
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9
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Jansson ET. Strategies for analysis of isomeric peptides. J Sep Sci 2017; 41:385-397. [PMID: 28922569 DOI: 10.1002/jssc.201700852] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/06/2017] [Accepted: 09/06/2017] [Indexed: 01/09/2023]
Abstract
This review presents an overview and recent progress of strategies for detecting isomerism in peptides, with focus on d/l epimerization and the various isomers that the presence of an aspartic acid residue may yield in a protein or peptide. While mass spectrometry has become a majorly used method of choice within proteomics, isomerism is inherently difficult to analyze because it is a modification that does not yield any change in mass of the analyte. Here, several techniques used for analysis of peptide isomerism are discussed, including enzymatic assays, liquid chromatography, and capillary electrophoresis. Recent progress in method development using mass spectrometry is also discussed, including labeling strategies, fragmentation techniques, and ion-mobility spectrometry.
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Affiliation(s)
- Erik T Jansson
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
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10
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Ahn SJ, Martin R, Rao S, Choi MY. Neuropeptides predicted from the transcriptome analysis of the gray garden slug Deroceras reticulatum. Peptides 2017; 93:51-65. [PMID: 28502716 DOI: 10.1016/j.peptides.2017.05.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 05/04/2017] [Accepted: 05/06/2017] [Indexed: 12/28/2022]
Abstract
The gray garden slug, Deroceras reticulatum (Gastropoda: Pulmonata), is one of the most common terrestrial molluscs. Research for this slug has focused mainly on its ecology, biology, and management due to the severe damage it causes on a wide range of vegetables and field crops. However, little is known about neuropeptides and hormonal signalings. This study, therefore, aimed to establish the transcriptome of D. reticulatum and to identify a comprehensive repertoire of neuropeptides in this slug. Illumina high-throughput sequencing of the whole body transcriptome of D. reticulatum generated a total of 5.9 billion raw paired-end reads. De novo assembly by Trinity resulted in 143,575 transcripts and further filtration selected 120,553 unigenes. Gene Ontology (GO) terms were assigned to 30,588 unigenes, composed of biological processes (36.9%), cellular components (30.2%) and molecular functions (32.9%). Functional annotation by BLASTx revealed 39,987 unigenes with hits, which were further categorized into important functional groups based on sequence abundance. Neuropeptides, ion channels, ribosomal proteins, G protein-coupled receptors, detoxification, immunity and cytoskeleton-related sequences were dominant among the transcripts. BLAST searches and PCR amplification were used to identify 65 putative neuropeptide precursor genes from the D. reticulatum transcriptome, which include achatin, AKH, allatostatin A, B and C, allatotropin, APGWamide, CCAP, cerebrin, conopressin, cysteine-knot protein hormones (bursicon alpha/beta and GPA2/GPB5), elevenin, FCAP, FFamide, FVamide (enterin, fulicin, MIP and PRQFVamide), GGNG, GnRH, insulin, NdWFamide, NKY, PKYMDT, PRXamide (myomodulin, pleurin and sCAP), RFamide (CCK/SK, FMRFamide, FxRIamide, LFRFamide, luqin and NPF), and tachykinin. Over 330 putative peptides were encoded by these precursors. Comparative analysis among different molluscan species clearly revealed that, while D. reticulatum neuropeptide sequences are conserved in Mollusca, there are also some unique features distinct from other members of this species. This is the first transcriptome-wide report of neuropeptides in terrestrial slugs. Our results provide comprehensive transcriptome data of the gray garden slug, with a more detailed focus on the rich repertoire of putative neuropeptide sequences, laying the foundation for molecular studies in this terrestrial slug pest.
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Affiliation(s)
- Seung-Joon Ahn
- USDA-ARS Horticultural Crops Research Unit,3420 NW Orchard Avenue, Corvallis, OR, 97330, USA; Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Ruth Martin
- USDA-ARS Forage Seed and Cereal Research Unit, 3450 SW Campus Way, Corvallis, OR, 97331, USA
| | - Sujaya Rao
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Man-Yeon Choi
- USDA-ARS Horticultural Crops Research Unit,3420 NW Orchard Avenue, Corvallis, OR, 97330, USA.
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11
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Evolutionarily conserved TRH neuropeptide pathway regulates growth in Caenorhabditis elegans. Proc Natl Acad Sci U S A 2017; 114:E4065-E4074. [PMID: 28461507 DOI: 10.1073/pnas.1617392114] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
In vertebrates thyrotropin-releasing hormone (TRH) is a highly conserved neuropeptide that exerts the hormonal control of thyroid-stimulating hormone (TSH) levels as well as neuromodulatory functions. However, a functional equivalent in protostomian animals remains unknown, although TRH receptors are conserved in proto- and deuterostomians. Here we identify a TRH-like neuropeptide precursor in Caenorhabditis elegans that belongs to a bilaterian family of TRH precursors. Using CRISPR/Cas9 and RNAi reverse genetics, we show that TRH-like neuropeptides, through the activation of their receptor TRHR-1, promote growth in Celegans TRH-like peptides from pharyngeal motor neurons are required for normal body size, and knockdown of their receptor in pharyngeal muscle cells reduces growth. Mutants deficient for TRH signaling have no defects in pharyngeal pumping or isthmus peristalsis rates, but their growth defect depends on the bacterial diet. In addition to the decrease in growth, trh-1 mutants have a reduced number of offspring. Our study suggests that TRH is an evolutionarily ancient neuropeptide, having its origin before the divergence of protostomes and deuterostomes, and may ancestrally have been involved in the control of postembryonic growth and reproduction.
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12
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Pang X, Jia C, Chen Z, Li L. Structural Characterization of Monomers and Oligomers of D-Amino Acid-Containing Peptides Using T-Wave Ion Mobility Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:110-118. [PMID: 27822705 PMCID: PMC5177490 DOI: 10.1007/s13361-016-1523-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/04/2016] [Accepted: 10/06/2016] [Indexed: 05/03/2023]
Abstract
The D-residues are crucial to biological function of D-amino acid containing peptides (DAACPs). Previous ion mobility mass spectrometry (IM-MS) studies revealing oligomerization patterns of amyloid cascade demonstrated conversion from native soluble unstructured assembly to fibril ß-sheet oligomers, which has been implicated in amyloid diseases, such as Alzheimer's disease and type 2 diabetes. Although neuropeptides are typically present at very low concentrations in circulation, their local concentrations could be much higher in large dense core vesicles, forming dimers or oligomers. We studied the oligomerization of protonated and metal-adducted achatin I and dermorphin peptide isomers with IM-MS. Our results suggested that dimerization, oligomerization, and metal adduction augment the structural differences between D/L peptide isomers compared to protonated monomers. Dimers and oligomers enhanced the structural differences between D/L peptide isomers in both aqueous and organic solvent system. Furthermore, some oligomer forms were only observed for either D- or L-isomers, indicating the importance of chiral center in oligomerization process. The oligomerization patterns of D/L isomers appear to be similar. Potassium adducts were detected to enlarge the structural differences between D/L isomers. Graphical Abstract ᅟ.
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Affiliation(s)
- Xueqin Pang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Chenxi Jia
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
- National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Beijing Institute of Radiation Medicine, Beijing, 102206, China
| | - Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- School of Life Sciences, Tianjin University, Tianjin, China.
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13
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Livnat I, Tai HC, Jansson ET, Bai L, Romanova EV, Chen TT, Yu K, Chen SA, Zhang Y, Wang ZY, Liu DD, Weiss KR, Jing J, Sweedler JV. A d-Amino Acid-Containing Neuropeptide Discovery Funnel. Anal Chem 2016; 88:11868-11876. [PMID: 27788334 PMCID: PMC5144109 DOI: 10.1021/acs.analchem.6b03658] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
A receptor binding
class of d-amino acid-containing peptides
(DAACPs) is formed in animals from an enzymatically mediated post-translational
modification of ribosomally translated all-l-amino acid peptides.
Although this modification can be required for biological actions,
detecting it is challenging because DAACPs have the same mass as their
all-l-amino acid counterparts. We developed a suite of mass
spectrometry (MS) protocols for the nontargeted discovery of DAACPs
and validated their effectiveness using neurons from Aplysia
californica. The approach involves the following three steps,
with each confirming and refining the hits found in the prior step.
The first step is screening for peptides resistant to digestion by
aminopeptidase M. The second verifies the presence of a chiral amino
acid via acid hydrolysis in deuterium chloride, labeling with Marfey’s
reagent, and liquid chromatography–mass spectrometry to determine
the chirality of each amino acid. The third involves synthesizing
the putative DAACPs and comparing them to the endogenous standards.
Advantages of the method, the d-amino acid-containing neuropeptide
discovery funnel, are that it is capable of detecting the d-form of any common chiral amino acid, and the first two steps do
not require peptide standards. Using these protocols, we report that
two peptides from the Aplysia achatin-like neuropeptide
precursor exist as GdYFD and SdYADSKDEESNAALSDFA.
Interestingly, GdYFD was bioactive in the Aplysia feeding and locomotor circuits but SdYADSKDEESNAALSDFA
was not. The discovery funnel provides an effective means to characterize
DAACPs in the nervous systems of animals in a nontargeted manner.
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Affiliation(s)
| | | | | | | | | | - Ting-Ting Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Ke Yu
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Song-An Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Yan Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Zheng-Yang Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Dan-Dan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Klaudiusz R Weiss
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Jian Jing
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University , Nanjing, Jiangsu 210046, China.,Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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14
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Nerve-granular cell communication in the atrium of the snail Achatina achatina occurs via the cardioexcitatory transmitters serotonin and FMRFamide. Cell Tissue Res 2016; 366:245-254. [PMID: 27660155 DOI: 10.1007/s00441-016-2483-x] [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: 03/07/2016] [Accepted: 07/20/2016] [Indexed: 10/21/2022]
Abstract
In the present study, the anatomical association and functional interaction between nerve fibres and granular cells in the atrium of the snail Achatina achatina are investigated using a combination of scanning electron microscopy (SEM), pharmacological and immunofluorescence techniques. The SEM studies support a close anatomical association of axons with granular cells and new features of surface morphology are revealed. Pharmacological experiments showed that both serotonin and FMRFamide were able to induce degranulation of granular cells and the release of cysteine-rich atrial secretory protein. Serotonin- and FMRFamide-immunoreactive nerve fibres were observed at variable distances from granular cells, ranging from close contact to distances as far as the diameter of a muscle bundle. These results suggest that serotonin and FMRFamide play a role as paracrine excitatory transmitters in nerve-to-granular cell communication.
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15
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Yang CY, Yu K, Wang Y, Chen SA, Liu DD, Wang ZY, Su YN, Yang SZ, Chen TT, Livnat I, Vilim FS, Cropper EC, Weiss KR, Sweedler JV, Jing J. Aplysia Locomotion: Network and Behavioral Actions of GdFFD, a D-Amino Acid-Containing Neuropeptide. PLoS One 2016; 11:e0147335. [PMID: 26796097 PMCID: PMC4721866 DOI: 10.1371/journal.pone.0147335] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 01/01/2016] [Indexed: 12/02/2022] Open
Abstract
One emerging principle is that neuromodulators, such as neuropeptides, regulate multiple behaviors, particularly motivated behaviors, e.g., feeding and locomotion. However, how neuromodulators act on multiple neural networks to exert their actions remains poorly understood. These actions depend on the chemical form of the peptide, e.g., an alternation of L- to D- form of an amino acid can endow the peptide with bioactivity, as is the case for the Aplysia peptide GdFFD (where dF indicates D-phenylalanine). GdFFD has been shown to act as an extrinsic neuromodulator in the feeding network, while the all L-amino acid form, GFFD, was not bioactive. Given that both GdFFD/GFFD are also present in pedal neurons that mediate locomotion, we sought to determine whether they impact locomotion. We first examined effects of both peptides on isolated ganglia, and monitored fictive programs using the parapedal commissural nerve (PPCN). Indeed, GdFFD was bioactive and GFFD was not. GdFFD increased the frequency with which neural activity was observed in the PPCN. In part, there was an increase in bursting spiking activity that resembled fictive locomotion. Additionally, there was significant activity between bursts. To determine how the peptide-induced activity in the isolated CNS is translated into behavior, we recorded animal movements, and developed a computer program to automatically track the animal and calculate the path of movement and velocity of locomotion. We found that GdFFD significantly reduced locomotion and induced a foot curl. These data suggest that the increase in PPCN activity observed in the isolated CNS during GdFFD application corresponds to a reduction, rather than an increase, in locomotion. In contrast, GFFD had no effect. Thus, our study suggests that GdFFD may act as an intrinsic neuromodulator in the Aplysia locomotor network. More generally, our study indicates that physiological and behavioral analyses should be combined to evaluate peptide actions.
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Affiliation(s)
- Chao-Yu Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Ke Yu
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Ye Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Song-An Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Dan-Dan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Zheng-Yang Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Yan-Nan Su
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Shao-Zhong Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Ting-Ting Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Itamar Livnat
- Beckman Institute for Advanced Science and Technology and Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Ferdinand S. Vilim
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Elizabeth C. Cropper
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Klaudiusz R. Weiss
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Jonathan V. Sweedler
- Beckman Institute for Advanced Science and Technology and Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jian Jing
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- * E-mail:
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16
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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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17
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Bai L, Livnat I, Romanova EV, Alexeeva V, Yau PM, Vilim FS, Weiss KR, Jing J, Sweedler JV. Characterization of GdFFD, a D-amino acid-containing neuropeptide that functions as an extrinsic modulator of the Aplysia feeding circuit. J Biol Chem 2013; 288:32837-51. [PMID: 24078634 DOI: 10.1074/jbc.m113.486670] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During eukaryotic translation, peptides/proteins are created using L-amino acids. However, a D-amino acid-containing peptide (DAACP) can be produced through post-translational modification via an isomerase enzyme. General approaches to identify novel DAACPs and investigate their function, particularly in specific neural circuits, are lacking. This is primarily due to the difficulty in characterizing this modification and due to the limited information on neural circuits in most species. We describe a multipronged approach to overcome these limitations using the sea slug Aplysia californica. Based on bioinformatics and homology to known DAACPs in the land snail Achatina fulica, we targeted two predicted peptides in Aplysia, GFFD, similar to achatin-I (GdFAD versus GFAD, where dF stands for D-phenylalanine), and YAEFLa, identical to fulyal (YdAEFLa versus YAEFLa), using stereoselective analytical methods, i.e. MALDI MS fragmentation analysis and LC-MS/MS. Although YAEFLa in Aplysia was detected only in an all L-form, we found that both GFFD and GdFFD were present in the Aplysia CNS. In situ hybridization and immunolabeling of GFFD/GdFFD-positive neurons and fibers suggested that GFFD/GdFFD might act as an extrinsic modulator of the feeding circuit. Consistent with this hypothesis, we found that GdFFD induced robust activity in the feeding circuit and elicited egestive motor patterns. In contrast, the peptide consisting of all L-amino acids, GFFD, was not bioactive. Our data indicate that the modification of an L-amino acid-containing neuropeptide to a DAACP is essential for peptide bioactivity in a motor circuit, and thus it provides a functional significance to this modification.
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Affiliation(s)
- Lu Bai
- From the Beckman Institute for Advanced Science and Technology and Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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18
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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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19
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Bai L, Romanova EV, Sweedler JV. Distinguishing endogenous D-amino acid-containing neuropeptides in individual neurons using tandem mass spectrometry. Anal Chem 2011; 83:2794-800. [PMID: 21388150 DOI: 10.1021/ac200142m] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
RNA-based protein synthesis produces L-amino acid-containing proteins and peptides. D-amino acid-containing peptides (DAACPs) can be generated from L-amino acid peptides via post-translational modification. In the nervous system, the conformational change of a single L-amino acid in a peptide to its D-form results in altered bioactivity, with some DAACPs having orders-of-magnitude enhanced efficacy. However, this modification is often overlooked when characterizing endogenous peptides. Here, with the use of matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF)/TOF mass spectrometry, neuropeptides that have the second residue isomerized to the D-isoform are distinguished from their L-epimers via differences in the relative amounts of specific fragment ions during tandem MS. With the appropriate fragment ions chosen, and in some cases with the use of metal adducts, epimer discrimination is optimized. Specifically, the cardioexcitatory peptide Asn-(D)Trp-Phe-amide (NdWFa) was assayed directly from neurons isolated from the sea slug Aplysia californica; the fraction of the peptide with the second residue (W) in the D- versus L-form was 90 ± 10%. We demonstrate that this approach is well suited for confirming DAACPs directly from cells and tissue, advancing our understanding of the l to d modification and the role it plays in cell-to-cell signaling.
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Affiliation(s)
- Lu Bai
- Department of Molecular and Integrative Physiology, University of Illinois, Urbana, Illinois 61801, USA
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20
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Martínez-Rodríguez S, Martínez-Gómez A, Rodríguez-Vico F, Clemente-Jiménez J, Las Heras-Vázquez F. Natural Occurrence and Industrial Applications of d-Amino Acids: An Overview. Chem Biodivers 2010; 7:1531-48. [DOI: 10.1002/cbdv.200900245] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Veenstra JA. Neurohormones and neuropeptides encoded by the genome of Lottia gigantea, with reference to other mollusks and insects. Gen Comp Endocrinol 2010; 167:86-103. [PMID: 20171220 DOI: 10.1016/j.ygcen.2010.02.010] [Citation(s) in RCA: 161] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 02/04/2010] [Accepted: 02/12/2010] [Indexed: 12/23/2022]
Abstract
The Lottia gigantea genome was prospected for the presence of genes coding neuropeptides and neurohormones. Four genes code insulin-related peptides: two genes code molluscan insulin-like growth hormones, one gene an insulin very similar to vertebrate insulin, and the fourth a peptide related to drosophila insulin-like peptide 7. Four other genes encode the cysteine-knot proteins GPA2/GPB5 and bursicon/parabursicon. Another 37 genes code for precursors of the following neuropeptides: achatin, APGWamide, allatostatin C, allatotropin, buccalin (perhaps an allatostatin A homolog), cerebrin, CCAP, conopressin, elevenin (the predicted neuropeptide made by abdominal neuron 11 in Aplysia), egg laying hormone (two genes), enterin, feeding circuit activating neuropeptide (FCAP), FFamide, FMRFamide, GGNG, a GnRH-like peptide, the newly discovered LASGLVamide, LFRFamide, LFRYamide, LRNFVamide, luqin, lymnokinin, myomodulin (two genes), the newly discovered NKY, NPY, pedal peptide (three genes), PKYMDT, pleurin, PXFVamide, small cardioactive peptides, tachykinins (two genes) and WWamide (an allatostatin B homolog). One gene was found to encode FWISamide, while about 20 closely related genes were found to encode WWFamide. These small neuropeptides appear homologous to the NdWFamide, which contains d-Trp; these genes are similar to the Aplysia gene encoding NWFamide. Some of these peptides had not been previously identified from mollusks, such as the predicted hormones similar to Drosophila and vertebrate insulins, bursicon, the putative proctolin homolog PKYMDT and allatostatin C. Together with neuropeptides which are likely homologs of other insect neuropeptides, such as cerebrin and WWamide, this shows that despite significant differences the molluscan and arthropod neuropeptidomes are more similar than generally recognized.
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Affiliation(s)
- Jan A Veenstra
- Université de Bordeaux, CNRS, CNIC UMR 5228, 33400 Talence, France.
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22
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Bai L, Sheeley S, Sweedler JV. Analysis of Endogenous D-Amino Acid-Containing Peptides in Metazoa. ACTA ACUST UNITED AC 2009; 1:7-24. [PMID: 20490347 DOI: 10.1007/s12566-009-0001-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Peptides are chiral molecules with their structure determined by the composition and configuration of their amino acid building blocks. The naturally occurring amino acids, except glycine, possess two chiral forms. This allows the formation of multiple peptide diastereomers that have the same sequence. Although living organisms use L-amino acids to make proteins, a group of D-amino acid-containing peptides (DAACPs) has been discovered in animals that have at least one of their residues isomerized to the D-form via an enzyme-catalyzed process. In many cases, the biological functions of these peptides are enhanced due to this structural conversion. These DAACPs are different from those known to occur in bacterial cell wall and antibiotic peptides, the latter of which are synthesized in a ribosome-independent manner. DAACPs have now also been identified in a number of distinct groups throughout the Metazoa. Their serendipitous discovery has often resulted from discrepancies observed in bioassays or in chromatographic behavior between natural peptide fractions and peptides synthesized according to a presumed all-L sequence. Because this L-to-D post-translational modification is subtle and not detectable by most sequence determination approaches, it is reasonable to suspect that many studies have overlooked this change; accordingly, DAACPs may be more prevalent than currently thought. Although diastereomer separation techniques developed with synthetic peptides in recent years have greatly aided in the discovery of natural DAACPs, there is a need for new, more robust methods for naturally complex samples. In this review, a brief history of DAACPs in animals is presented, followed by discussion of a variety of analytical methods that have been used for diastereomeric separation and detection of peptides.
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Affiliation(s)
- Lu Bai
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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23
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Song Y, Liu YM. Quantitation of cardioexcitatory Asn-D-Trp-Phe-NH2 diastereomers in Aplysia's central nervous system by nanoscale liquid chromatography-tandem mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2008; 43:1285-1290. [PMID: 18416437 DOI: 10.1002/jms.1408] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A tripeptide, Asn-D-Trp-Phe-NH(2) (NdWFa) that contains a D-amino acid residue (i.e. D-tryptophan) was previously identified in Aplysia's central nervous system (CNS) and found to be cardioexcitatory. However, the occurrence of its diastereomers including NWFa, theoretically the precursor of NdWFa, remains largely unknown. In this work, a nanoscale liquid chromatographic/tandem mass spectrometric (nano-LC-MS/MS) method was developed for a sensitive determination of the diastereomers of NWFa. Resolution of the diastereomers including NWFa, NdWFa, NWdFa, and dNWFa was achieved on capillary columns packed with C(18) silica particles with an MS detection-friendly mobile phase consisting of water, acetonitrile, and formic acid. Columns of different internal diameters (IDs) ranging from 75 to 250 microm were evaluated to achieve the best sensitivity. With the use of a 75 microm ID column integrated with a nanoelectrospray emitter, the method had limits of detection (LOD) of 0.21 nM (or 0.49 pg on column, 5 microl injected) NdWFa in tissue homogenate (S/N=3). The five major ganglia in Aplysia californica's CNS (i.e. buccal, cerebral, abdominal, plural, and pedal) were analyzed. NdWFa was detected only in abdominal ganglion at the ng/g tissue level. Further, its diastereomer, NWFa, was also detected for the first time and also only in abdominal ganglion at a significantly lower level. The levels of both NWFa and NdWFa varied from animal to animal in the range from 0 to 81 ng/g tissue.
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Affiliation(s)
- Yaru Song
- Department of Chemistry, Jackson State University, Jackson, MS 39217, USA
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24
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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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25
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Sheeley SA, Miao H, Ewing MA, Rubakhin SS, Sweedler JV. Measuring D-amino acid-containing neuropeptides with capillary electrophoresis. Analyst 2005; 130:1198-203. [PMID: 16021220 DOI: 10.1039/b504717j] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Neuropeptides are heavily posttranslationally modified (PTM) gene products that are often characterized by a variety of mass spectrometric approaches. Recently, the occurrence of amino acids in the D-form has been documented in several neuropeptides. As this modification has no associated mass shift, this particular PTM is difficult to evaluate using mass spectrometry (MS) alone. Here we demonstrate several approaches using capillary electrophoresis (CE) with absorbance and laser-induced fluorescence (LIF) for the separation of native and derivatized molluscan peptides containing D-amino acids. The combination of peptide derivatization followed by CE/LIF is well suited for single cell measurements because of its ability to characterize the peptides in such small samples. In order to verify this approach, the D-Trp-containing peptide NdWFa (NH2-Asn-D-Trp-Phe-CONH2), present in individual neurons from the marine mollusk Aplysia californica, has been characterized. The mass spectra show that NdWFa and/or NWFa are present in specific neurons; CE/LIF analysis of these cells demonstrates that NdWFa is the dominant form of the peptide.
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Affiliation(s)
- Sarah A Sheeley
- Department of Chemistry & Beckman Institute, University of Illinois, 600 South Mathews Ave., 63-5, Urbana, IL 61801, USA
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26
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Morishita F, Minakata H, Sasaki K, Tada K, Furukawa Y, Matsushima O, Mukai ST, Saleuddin ASM. Distribution and function of an Aplysia cardioexcitatory peptide, NdWFamide, in pulmonate snails. Peptides 2003; 24:1533-44. [PMID: 14706532 DOI: 10.1016/j.peptides.2003.07.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The distribution and function of an Aplysia cardioexcitatory peptide, NdWFamide, were examined in the nervous system of pulmonate snails. We chemically identified the authentic NdWFamide from a land snail (Euhadra congenita) and a freshwater snail (Lymnaea stagnalis). NdWFamide potentiated the heartbeat of those snails. Immunohistochemistry using anti-NdWFamide antibody demonstrated the distribution of NdWFamide-containing neurons and fibers in the central nervous system, as well as peripheral tissues, such as the cardiovascular region and accessory sex organs. These results suggest that NdWFamide is a neuropeptide mediating the neural regulation of the activity of the cardiovascular and reproductive systems of snails.
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Affiliation(s)
- F Morishita
- Department of Biological Science, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8526, Hiroshima, Japan.
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27
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Baek DH, Kwon SJ, Hong SP, Kwak MS, Lee MH, Song JJ, Lee SG, Yoon KH, Sung MH. Characterization of a thermostable D-stereospecific alanine amidase from Brevibacillus borstelensis BCS-1. Appl Environ Microbiol 2003; 69:980-6. [PMID: 12571020 PMCID: PMC143600 DOI: 10.1128/aem.69.2.980-986.2003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A gene encoding a new thermostable D-stereospecific alanine amidase from the thermophile Brevibacillus borstelensis BCS-1 was cloned and sequenced. The molecular mass of the purified enzyme was estimated to be 199 kDa after gel filtration chromatography and about 30 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, indicating that the enzyme could be composed of a hexamer with identical subunits. The purified enzyme exhibited strong amidase activity towards D-amino acid-containing aromatic, aliphatic, and branched amino acid amides yet exhibited no enzyme activity towards L-amino acid amides, D-amino acid-containing peptides, and NH(2)-terminally protected amino acid amides. The optimum temperature and pH for the enzyme activity were 85 degrees C and 9.0, respectively. The enzyme remained stable within a broad pH range from 7.0 to 10.0. The enzyme was inhibited by dithiothreitol, 2-mercaptoethanol, and EDTA yet was strongly activated by Co(2+) and Mn(2+). The k(cat)/K(m) for D-alaninamide was measured as 544.4 +/- 5.5 mM(-1) min(-1) at 50 degrees C with 1 mM Co(2+).
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Affiliation(s)
- Dae Heoun Baek
- Biocatalysis Research Laboratory, National Research Laboratory, Korea Research Institute of Bioscience and Biotechnology, Yuseong, Daejeon 305-333, Korea
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28
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Baek DH, Song JJ, Lee SG, Kwon SJ, Asano Y, Sung MH. New thermostable d-methionine amidase from Brevibacillus borstelensis BCS-1 and its application for d-phenylalanine production. Enzyme Microb Technol 2003. [DOI: 10.1016/s0141-0229(02)00268-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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29
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Muneoka Y, Morishita F, Furukawa Y, Matsushima O, Kobayashi M, Ohtani M, Takahashi T, Iwakoshi E, Fujisawa Y, Minakata H. Comparative Aspects of Invertebrate Neuropeptides. ACTA BIOLOGICA HUNGARICA 2000. [DOI: 10.1007/bf03543211] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Abstract
Fulicin is a D-amino acid-containing neuropeptide that has been thought to control male copulatory behavior in the land snail, Achatina fulica. In the present study, we demonstrated that the vagina and the oviduct of Achatina were densely innervated by fulicin-like immunoreactive neuronal fibers. We confirmed that fulicin was actually present in the vagina by mass spectrometry. Furthermore, fulicin showed a profound excitatory effect on contractions of the vagina and the oviduct. These results suggest that fulicin controls female egg-laying behavior as an excitatory neuropeptide regulating the female reproductive organs of the snail.
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Affiliation(s)
- Y Fujisawa
- Suntory Institute for Bioorganic Research, 1-1-1, Wakayamadai, Shimamoto, Mishima, Osaka 618-8503, Japan.
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31
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Abstract
Octopus cardioactive peptides (Ocp-1: Gly-D-Phe-Gly-Asp, and Ocp-3: Gly-Ser-Trp-Asp) were isolated from brain extracts of the octopus, Octopus minor, using the isolated systemic heart as a bioassay. These peptides showed both positive chronotropic and inotropic effects on the heart. The stereoisomers at position 2 were also isolated, but their activities were only 1/10(3)-1/10(4) those of the corresponding isomers. The presence of the peptides in the systemic heart was confirmed by time-of-flight mass spectrometry (MS) and tandem MS analysis. The results suggested that Ocp-1 and Ocp-3 might be involved in excitatory control of the octopus cardiovascular system as neuropeptides and/or neurohormones.
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Affiliation(s)
- E Iwakoshi
- Suntory Institute for Bioorganic Research, 618-8503, Osaka, Japan
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32
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Satake H, Takuwa K, Minakata H. Characterization of cDNA and expression of mRNA encoding an Achatina cardioexcitatory RFamide peptide. Peptides 1999; 20:1295-302. [PMID: 10612443 DOI: 10.1016/s0196-9781(99)00134-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Achatina cardioexcitatory peptide-1 (ACEP-1) is an RFamide family peptide isolated from the atria of the African giant snail, Achatina fulica. In this report, we describe an identification of the ACEP-1 cDNA sequence and localizations of the ACEP-1 mRNA. Southern blot analysis revealed that the ACEP-1 mRNA was present in the atrium as well as in the central nervous system. Furthermore, in situ hybridization revealed the localizations of the ACEP-1 mRNA in small neurons of the cerebral and pedal ganglia and a few large neurons of the right parietal and visceral ganglia.
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Affiliation(s)
- H Satake
- Suntory Institute for Bioorganic Research, Mishima-gun, Osaka, Japan
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33
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Friedman M. Chemistry, nutrition, and microbiology of D-amino acids. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 1999; 47:3457-3479. [PMID: 10552672 DOI: 10.1021/jf990080u] [Citation(s) in RCA: 278] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Exposure of food proteins to certain processing conditions induces two major chemical changes: racemization of all L-amino acids to D-isomers and concurrent formation of cross-linked amino acids such as lysinoalanine. Racemization of L-amino acids residues to their D-isomers in food and other proteins is pH-, time-, and temperature-dependent. Although racemization rates of the 18 different L-amino acid residues in a protein vary, the relative rates in different proteins are similar. The diet contains both processing-induced and naturally formed D-amino acids. The latter include those found in microorganisms, plants, and marine invertebrates. Racemization impairs digestibility and nutritional quality. The nutritional utilization of different D-amino acids varies widely in animals and humans. In addition, some D-amino acids may be both beneficial and deleterious. Thus, although D-phenylalanine in an all-amino-acid diet is utilized as a nutritional source of L-phenylalanine, high concentrations of D-tyrosine in such diets inhibit the growth of mice. Both D-serine and lysinoalanine induce histological changes in the rat kidney. The wide variation in the utilization of D-amino acids is illustrated by the fact that whereas D-methionine is largely utilized as a nutritional source of the L-isomer, D-lysine is totally devoid of any nutritional value. Similarly, although L-cysteine has a sparing effect on L-methionine when fed to mice, D-cysteine does not. Because D-amino acids are consumed by animals and humans as part of their normal diets, a need exists to develop a better understanding of their roles in nutrition, food safety, microbiology, physiology, and medicine. To contribute to this effort, this multidiscipline-oriented overview surveys our present knowledge of the chemistry, nutrition, safety, microbiology, and pharmacology of D-amino acids. Also covered are the origin and distribution of D-amino acids in the food chain and in body fluids and tissues and recommendations for future research in each of these areas. Understanding of the integrated, beneficial effects of D-amino acids against cancer, schizophrenia, and infection, and overlapping aspects of the formation, occurrence, and biological functions of D-amino should lead to better foods and improved human health.
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Affiliation(s)
- M Friedman
- Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 800 Buchanan Street, Albany, California 94710, USA.
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34
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Satake H, Yasuda-Kamatani Y, Takuwa K, Nomoto K, Minakata H, Nagahama T, Nakabayashi K, Matsushima O. Characterization of a cDNA encoding a precursor polypeptide of a D-amino acid-containing peptide, achatin-I and localized expression of the achatin-I and fulicin genes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 261:130-6. [PMID: 10103043 DOI: 10.1046/j.1432-1327.1999.00252.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Achatin-I and fulicin, isolated from the ganglia and atria of the giant land snail Achatina fulica, are a tetrapeptide and pentapeptide containing a d-Phe and d-Asn at position 2, respectively. We succeeded in cloning a cDNA encoding a precursor of achatin-I from the Achatina ganglia, revealing that the d-Phe present in achatin-I is coded by a common l-Phe codon, TTT or TTC. The deduced polypeptide was found to comprise seven repeats of the achatin sequence GFAD and one analog GFGD flanked on both sides by the typical endoproteolytic site KR. Northern blot analysis of transcripts and Southern blot analysis of reverse transcription (RT)-PCR products demonstrated that achatin-I mRNA was localized in the subesophageal ganglia, whereas expression of fulicin mRNA was detected in the atrium as well as in the subesophageal ganglia. Furthermore, localization of the achatin gene transcript in the right and left pedal ganglia compartments was shown by in situ hybridization on sections of subesophageal ganglia, whereas the fulicin transcript was observed in the right and left parietal ganglia. These data suggested that achatin-I plays an essential role in the regulation of the heart as a neurotransmitter or neurohormone through production in the pedal ganglia and transport to the atrium, whereas fulicin serves not only as a neurotransmitter or neurohormone but also as a novel atrial hormone.
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Affiliation(s)
- H Satake
- Suntory Institute for Bioorganic Research, Osaka, Japan
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35
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Volkmann RA, Heck SD. Biosynthesis of D-amino acid-containing peptides: exploring the role of peptide isomerases. EXS 1999; 85:87-105. [PMID: 9949870 DOI: 10.1007/978-3-0348-8837-0_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The discovery of D-amino acid residues in a growing number of gene-encoded peptides suggests that such biochemical modifications are more common than initially thought. In fact, the extent to which D-amino acids are incorporated into peptides by multicellular organisms probably has not been fully realized, since routine Edman sequencing does not provide the absolute stereochemistry of amino acid residues. Unless both the D and L isomers of a particular peptide sequence are isolated, D-amino acid-containing peptides are often identified only after synthesis of naturally-occurring peptide fails to yield the desired activity. To date, D-amino acid residues (e.g., alanine, methionine, leucine, isoleucine, phenyl alanine, asparagine, tryptophan and serine) have been identified in peptides from a variety of species, including frogs, snails, clams, lobsters and spiders. While most have a single D-amino acid residue located near their N-termini, an exception is found with omega-Aga IVB. The examples highlighted in this chapter are the result of a unique strategy of multicellular organisms to circumvent stereochemical limitations imposed by the genetic code in an effort to increase molecular diversity. The presence of D-amino acids permits the generation of novel tertiary structure that could not be accessed from L-amino acids alone. Moreover, advantages of increased potency and protease stability are often observed. Our understanding of the biosynthesis of these D-amino acid-containing peptides is still in its infancy. Nevertheless, the discovery of a novel peptide isomerase from the venom of the Agelenopsis aperta spider provides some important clues to explain the incorporation of single D-amino acid residues within a peptide chain. Given its high homology with other serine proteases, the isomerase may represent an opportune mutation in response to evolutionary pressures. Yet, is the isomerase a unique exception or simply the first in a class of enzymes of varying substrate specificity capable of synthesizing D-amino acid-containing peptides? To be sure, much more remains to be explored about the precise timing and mechanism of the isomerization process, in addition to obtaining further structural data on the enzyme itself. Therein lies the continuation of this fascinating story in enzyme biochemistry.
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36
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Yasuda-Kamatani Y. Molluscan neuropeptides. EXS 1998; 85:37-56. [PMID: 9949867 DOI: 10.1007/978-3-0348-8837-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Achatin-I, fulicin, fulyal, Mytilus-FFRFamide and Helix CCAP-RP-III are D-amino acid-containing neuropeptides from molluscs. Achatin-I, fulicin and fulyal from Achatina showed excitatory and/or modulatory actions on the penis retractor, radula retractor or ventricular muscles and neurons, though their L isomers were devoid of activity. On the other hand, both Mytilus-FFRFamide and its L isomer showed excitatory effects on the anterior byssus retractor muscle. Moreover, in contrast to Achatina neuropeptides, Helix CCAP-RP-III exhibited no remarkable activities on any of the muscles tested; instead, its L isomer possessed various excitatory effects. The molecular structures of these short peptides would be affected by the L-->D conversion and could influence activity. Molecular biological studies on the fulicin precursor suggest that fulicin, fulyal and related peptides are produced in Achatina ganglia and heart by processing of the ribosomally made precursor, and that L-isomeric fulicin and fulyal further undergo epimerization to yield the D-isomers.
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37
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Morishita F, Nakanishi Y, Kaku S, Furukawa Y, Ohta S, Hirata T, Ohtani M, Fujisawa Y, Muneoka Y, Matsushima O. A novel D-amino-acid-containing peptide isolated from Aplysia heart. Biochem Biophys Res Commun 1997; 240:354-8. [PMID: 9388481 DOI: 10.1006/bbrc.1997.7659] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A novel cardio-excitatory peptide was purified from the hearts of Aplysia kurodai. The peptide was a tripeptide containing a D-amino acid residue in the second position, Asn-D-Trp-Phe-NH2 (NdWFamide). NdWFamide increased the amplitude of contractions of the perfused Aplysia heart with little effect on beating frequency, showing a threshold of approximately 10(-11) M. The peptide also potentiated spontaneous contractions of the anterior aorta. The synthetic peptide having L-Trp instead of D-Trp was about 1,000 times less potent than the native one. NdWFamide seems to play an important role in regulation of cardiac activity in Aplysia.
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Affiliation(s)
- F Morishita
- Department of Biological Science, Faculty of Science, Hiroshima University, Japan.
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