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Published online before print
November 19, 2007, 10.1101/gr.6714008 Genome Res. 18:113-122, 2008 ©2008 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/08 $5.00
Letter Genomics, transcriptomics, and peptidomics of neuropeptides and protein hormones in the red flour beetle Tribolium castaneum1 Department of Entomology, Kansas State University, Manhattan, Kansas 66506-4004, USA; 2 Institute of Zoology, University of Jena, D-07743 Jena, Germany; 3 Center for Functional and Comparative Insect Genomics and Department of Cell Biology and Comparative Zoology, Institute of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark; 4 National Institute of Agrobiological Science, Division of Insect Science, Tsukuba, Ibaraki 305-8634, Japan; 5 Department of Biochemistry, Kansas State University, Manhattan, Kansas 66506-4004, USA; 6 Department of Animal Physiology and Neurobiology, University of Leuven, BE-3000 Leuven, Belgium; 7 Department of Animal Physiology, University of Marburg, D-35032 Marburg, Germany
Neuropeptides and protein hormones are ancient molecules that mediate cell-to-cell communication. The whole genome sequence from the red flour beetle Tribolium castaneum, along with those from other insect species, provides an opportunity to study the evolution of the genes encoding neuropeptide and protein hormones. We identified 41 of these genes in the Tribolium genome by using a combination of bioinformatic and peptidomic approaches. These genes encode >80 mature neuropeptides and protein hormones, 49 peptides of which were experimentally identified by peptidomics of the central nervous system and other neuroendocrine organs. Twenty-three genes have orthologs in Drosophila melanogaster: Sixteen genes in five different groups are likely the result of recent gene expansions during beetle evolution. These five groups contain peptides related to antidiuretic factor-b (ADF-b), CRF-like diuretic hormone (DH37 and DH47 of Tribolium), adipokinetic hormone (AKH), eclosion hormone, and insulin-like peptide. In addition, we found a gene encoding an arginine-vasopressin-like (AVPL) peptide and one for its receptor. Both genes occur only in Tribolium and not in other holometabolous insects with a sequenced genome. The presence of many additional osmoregulatory peptides in Tribolium agrees well with its ability to live in very dry surroundings. In contrast to these extra genes, there are at least nine neuropeptide genes missing in Tribolium, including the genes encoding the prepropeptides for corazonin, kinin, and allatostatin-A. The cognate receptor genes for these three peptides also appear to be absent in the Tribolium genome. Our analysis of Tribolium indicates that, during insect evolution, genes for neuropeptides and protein hormones are often duplicated or lost.
Multicellular organisms use signaling molecules for cell-to-cell communication. Important among these signaling molecules are peptides and protein hormones which are produced in endocrine cells or neurons as larger precursors. These precursors (prepropeptides) are cleaved and further modified to yield mature peptides that are secreted into the extracellular environment. Peptides exert their action by binding to membrane receptors, mostly being G-protein coupled receptors (GPCRs), although some of them are receptor tyrosine kinases.
Studies of a number of insect species have provided invaluable information for understanding the function and the evolution of neuropeptides. Earlier studies on insect neuropeptides have used large physiological model species (i.e., locust, cockroach, and moth), and these have provided the groundwork for identifying the active signaling molecules. Further characterization of the functions of neuropeptides has been provided by recent genetic studies in Drosophila melanogaster, examining the genetic null mutants and cell ablations of specific peptidergic cells (McNabb et al. 1997
The earliest traceable representatives of ancestral neuropeptides and endocrine protein hormones date back to the most primitive metazoans, such as cnidarians (Grimmelikhuijzen et al. 2002
Ortholog neuropeptide genes show a high degree of divergence in their overall amino acid sequences while only small portions of the genes have been highly conserved, namely, those regions coding for mature peptides or even only the motif within the peptide sequence that is required for biological activity (Liu et al. 2006a
Another powerful approach to gain insight in the evolution of peptidergic signaling systems is based on the phylogeny of the cognate receptors for the neuropeptide ligands. G-proteincoupled receptors are large transmembrane proteins that have been well conserved and that carry more informative sequences allowing the evolutionary analysis of the respective genes. This phylogenetic analysis, which of course assumes that ligands and cognate receptors co-evolve, allows evolutionary grouping of insect neuropeptides (Park et al. 2002b
New techniques have recently emerged to identify the genes encoding neuropeptides. These new approaches include bioinformatic tools to predict the genes encoding neuropeptides from whole genome sequences and expressed sequence tag (EST) libraries, and direct detection of the processed mature peptides, using mass spectrometry (MS), also known as peptidomics (Hewes and Taghert 2001
Genomic studies in the fruit fly, malaria mosquito, and honeybee have been highly successful and have identified 31, 32, and 36 neuropeptide genes, respectively (Hewes and Taghert 2001
The current version of the genome sequence for Tribolium covers >95% of the total genome with >16,500 genes in the computerized annotation (Tribolium Genome Sequencing Consortium, in prep.). Homology-based searches of neuropeptide and protein hormone genes identified 41 genes encoding >80 mature peptides carrying the typical signatures of neuropeptides. Tribolium EST database searches and RT-PCR on a subset of genes confirmed the existence of transcripts for 20 of these genes (Table 1; Supplemental Data 1). By using different mass spectrometric methods, the presence of 71 mature/processed peptides (with truncated and repetitive sequences), derived from 20 genes, was detected (Supplemental Data 2). Altogether, the expression of 30 neuropeptide genes was confirmed using these methods. Table 1 also shows the putative cognate Tribolium GPCRs for these peptides (Hauser et al. 2007
Mass spectrometric analyses In insects, the majority of the known bioactive neuropeptides contain a carboxy-terminal amide group (derived from a glycine residue preceding the cleavage sites in the precursor) which is important for their bioactivity and biostability (Eipper et al. 1993
There are two genes in the upper group of Table 1, AKH-1 and AKH-3, for which we could not detect the predicted amidated neuropeptides by MS. Furthermore, a putative pyrokinin with the C-terminal WFGPRLamide sequence (also named CAPA-pyrokinin, which is pyrokinin encoded by the capa-gene [Predel and Wegener 2006
Conserved and orthologous neuropeptide genes Most Tribolium neuropeptides and protein hormone sequences have clear counterparts in other insect species (Table 1), which can be identified by conserved sequence motifs, implying that parts of their genes may be under strong evolutionary pressure to be conserved.
Also the structure of the prepropeptide is often highly conserved in terms of the location of the immature peptides. For example, in the prepropeptide of adipokinetic hormone, proctolin, and SIFamide (Supplemental Data 1), the short neuropeptide sequences (5–12 amino acid residues long) are located immediately after the N-terminal signal peptide and are tailed by longer associated peptides ( Multiple repeated similar peptide sequences separated by cleavage sites are typical of other prepropeptides, including FMRFamide, allatostatin-B, CAPA, pyrokinin, and TKRPs with six, six, four, five, and eight repeats, respectively, in Tribolium (Supplemental Data 1). The numbers of repeats among the orthologs in different insect species may vary. For example, the allatostatin-B (also referred to as myoinhibitory peptide MIP), has six repeats in Tribolium but five, four, and thirteen repeats in D. melanogaster, Anopheles gambiae, and Bombyx mori, respectively.
The conservation of neuropeptide gene structure is extended to the conservation of alternative splicing patterns. For the ion transport peptide and the DH genes, for example, mutually exclusive ways of alternative splicing are conserved in several insect orders (Dai et al. 2007
Insulin-like peptides and neuroparsin
The largest group, ILP-B, contains highly diverse genes including recently duplicated genes in mosquitoes (AgILP1 and AgILP7, and AgILP3 and AgILP6 in Fig. 2). Phylogenetic analysis within the group was not successful because of the highly diverged sequences resulting in a low statistical support for most of the clades. However, a strict conservation of the cysteine motif CCxxxC (also typical for vertebrate insulins) was found in the A chain. The ILP-B group includes the multiple copies of bombyxin-like peptides, which have originally been isolated from the silkworm brain (Nagasawa et al. 1986
By contrast, the ILP-A and -C groups are characterized by the CCxxxxC-motif, with four amino acids between the cysteine residues. All insect ILP-A members display high sequence homology, particularly of the A- and B-chain regions. The ILP-A group has not been identified in the honeybee nor in the silkworm genomes. The ILP-C group is further characterized by a very short or absent C-peptide between the A- and B-chains and a single putative mono- or dibasic cleavage signal between the A- and B- chains (Fig. 2). The ILP-C group comprises mammalian insulin-like growth factors (i.e., IGF-1b of human P05019
[GenBank]
) and a large number of ILPs (named INS) in Caenorhabditis elegans (Duret et al. 1998
Neuroparsins are structurally similar to the mosquito ovary ecdysteroidogenic hormone and to the vertebrate insulin-like growth factor binding proteins (Schoofs et al. 1997
Novel osmoregulatory neuropeptide genes in Tribolium The Tribolium genome revealed three groups of osmoregulatory neuropeptide genes: One gene encoding an arginine vasopressin-like peptide (AVPL), five genes encoding antidiuretic factors (ADFs), and one gene giving rise, by alternative splicing, to two corticotropin releasing factor (CRF)-like diuretic hormones DH37 and DH47.
The gene encoding AVPL is absent in all other holometabolous insects with a sequenced genome (Table 1). In addition, an AVPL GPCR has been identified in Tribolium, which is also not found in other holometabolous insects (Hauser et al. 2007
The first evidence for an AVPL in insects was revealed by an antibody raised against vertebrate AVP, which stained neurosecretory cells in the CNS of locusts (Proux and Rougon-Rapuzzi 1980
The other group of peptides, ADFs, was known only from a very closely related beetle, Tenebrio molitor, which, like Tribolium, also lives in very dry ecosystems. In T. molitor, two ADFs (ADFa and ADFb) inhibit diuretic activity of the Malpighian tubules (Eigenheer et al. 2002
There are two diuretic hormone genes in Tribolium, one yielding DH31 and one yielding two different, but homologous CRF-like diuretic hormones, DH37 and DH47 (Supplemental Data 1). DH37 and DH47 are encoded by two separate exons that are alternatively spliced to a common 5' exon encoding the signal peptide (Fig. 6). This alternative splicing is not found in Drosophila, where there is only one CRF-like diuretic hormone DH44 (Cabrero et al. 2002
The amino acid sequence of Tribolium DH47 is identical to that of the previously isolated DH47 from T. molitor (Furuya et al. 1998
Putative neuropeptide genes in Tribolium
Several peptides identified in a recent peptidomics study of the honeybee have been tentatively named after their partial N-terminal peptide sequences, i.e., NVP-containing, IDL-containing, and ITG-containing peptides (Hummon et al. 2006
Expansions of neuropeptide genes in Tribolium Three genes for AKH-like peptides were found in the Tribolium genome. Predicted prepropeptides have common structures with signal peptides for secretion directly followed by the immature peptides and an additional C-terminal conserved region surrounding two conserved cysteines. The two Tribolium AKHs—TcAKH1 and TcAKH2—are similar to each other, while another containing TcAKH3 is more divergent and has mild homology with the sequences found in mosquito species (Fig. 7). Sequence similarity among different insect AKH prepropeptides suggests that there are at least two distinct ancestral forms. The Drosophila genome contains only one AKH gene copy, which implies the loss of at least one lineage in Drosophila. AKHs of insects are usually synthesized in the glandular portion of the corpora cardiaca (CC) but not in the central nervous system itself. Direct profiling of the CC by MALDI-MS as well as analyses of CC-extracts by ESI-MS revealed the expression of AKH-2, whereas AKH-1 and AKH-3 could not be observed.
Eclosion hormone (EH) is known for its involvement in ecdysis behavior (Truman 2005
Neuropeptide genes lacking in Tribolium Several neuropeptide genes are apparently lacking in the Tribolium genome. These include neuropeptide F, pigment dispersing factor (PDF), ADF-a, orcokinin, corazonin, kinin, and allatostatin-A. Interestingly, for the latter three, their cognate GPCRs also have not been found in the Tribolium genome (Hauser et al. 2007
Gene identification The whole genome sequence of Tribolium castaneum, version 2.0, was used for the homology searches at the Web site of the Human Genome Sequence Center, Baylor College of Medicine (http://www.hgsc.bcm.tmc.edu/blast/blast.cgi?organism=Tcastaneum), or in the local BLAST by using Blosum62 or PAM30 for searching the short matching sequences. Prediction of the gene structure and open reading frame was done in GENBOREE (http://www.genboree.org) that contains the GLEAN2 predictions incorporating the results from multiple gene-prediction software programs and by manual correction. The homology search was followed by a prediction of the gene structure. The signal peptide in the N-terminal was predicted by the SIGNALP server (Bendtsen et al. 2004
Mining EST data was done using the NCBI non-redundant database and trace archives (http://www.ncbi.nlm.nih.gov/Traces/trace.cgi). RT-PCR to confirm the presence of transcripts was applied using the primers designed on the highly conserved regions in the gene predictions. Details of primer information will be published elsewhere. Multiple sequence alignment was performed in ClustalW (http://www.ebi.ac.uk/clustalw/) (Thompson et al. 1994
The transcript of each gene was confirmed by either reverse transcription PCR or EST sequences (http://www.ncbi.nlm.nih.gov/dbEST/index.html; Park et al. 2007)
Sample preparation for MS Different parts of the CNS and peptide release sites (retrocerebral complex, thoracic perisympathetic organs, abdominal perisympathetic organs, Inka cells) were first directly analyzed on a MALDI-TOF mass spectrometer. The resulting ion signals were compared with the theoretical masses of the predicted peptides. A number of ions could be fragmented on the matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS, but most of the fragmentations were subsequently done using an ESI-Q-TOF MS and extracts of 30 brains, 30 thoracic ganglia, and 50 corpora cardiaca, respectively.
Dissection of nervous tissues was performed as described for D. melanogaster (Predel et al. 2004
MALDI-TOF MS
ESI-Q-TOF MS
This study was funded by USDA-NRI-CRSEES 2007-35604-17759, NSF IOS-0615818, the German Research Foundation (Predel 595/6-4), Danish Research Agency, and Novo Nordisk Foundation. P.V. is a postdoctoral fellow of the Fund for Scientific Research Flanders (F.W.O. Vlaanderen). The publication is Contribution Number 07-229-J from Kansas Agricultural Experimental Station.
8 Corresponding author.
E-mail ypark{at}ksu.edu; fax (785) 532-6232. [Supplemental material is available online at www.genome.org.] Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.6714008
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Received May 15, 2007; accepted in revised format August 6, 2007. This article has been cited by other articles:
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