Summary: Galanin message associated peptide (GMAP)
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Galanin Edit Wikipedia article
|, GAL-GMAP, GALN, GLNN, GMAP, ETL8, galanin and GMAP prepropeptide|
|Chemical and physical data|
|Molar mass||3210.56 g/mol|
|(what is this?)|
Galanin is a neuropeptide encoded by the GAL gene, that is widely expressed in the brain, spinal cord, and gut of humans as well as other mammals. Galanin signaling occurs through three G protein-coupled receptors.
The functional role of galanin remains largely unknown; however, galanin is predominantly involved in the modulation and inhibition of action potentials in neurons. Galanin has been implicated in many biologically diverse functions, including: nociception, waking and sleep regulation, cognition, feeding, regulation of mood, regulation of blood pressure, it also has roles in development as well as acting as a trophic factor. Galanin neurons in the medial preoptic area of the hypothalamus may govern parental behaviour. Galanin is linked to a number of diseases including Alzheimer's disease, epilepsy as well as depression, eating disorders and cancer. Galanin appears to have neuroprotective activity as its biosynthesis is increased 2-10 fold upon axotomy in the peripheral nervous system as well as when seizure activity occurs in the brain. It may also promote neurogenesis.
Galanin is predominantly an inhibitory, hyperpolarizing neuropeptide and as such inhibits neurotransmitter release. Galanin is often co-localized with classical neurotransmitters such as acetylcholine, serotonin, and norepinephrine, and also with other neuromodulators such as neuropeptide Y, substance P, and vasoactive intestinal peptide.
Galanin was first identified from porcine intestinal extracts in 1978 by Professor Viktor Mutt and colleagues at the Karolinska Institute, Sweden using a chemical assay technique that detects peptides according to its C-terminal alanine amide structure. Galanin is so-called because it contains an N-terminal glycine residue and a C-terminal alanine. The structure of galanin was determined in 1983 by the same team, and the cDNA of galanin was cloned from a rat anterior pituitary library in 1987.
Galanin is located predominantly in the central nervous system and gastrointestinal tract. Within the central nervous system, highest concentrations are found in the hypothalamus, with lower levels in the cortex and brainstem. Gastrointestinal galanin is most abundant in the duodenum, with lower concentrations in the stomach, small intestine, and colon.
|Pig||G W T L N||S A G Y L||L G P H A||I D N H R||S F H D K||Y G L A *|
|Human||G W T L N||S A G Y L||L G P H A||V G N H R||S F S D K||N G L T S **|
|Cow||G W T L N||S A G Y L||L G P H A||L D S H R||S F Q D K||H G L A *|
|Rat||G W T L N||S A G Y L||L G P H A||I D N H R||S F S D K||H G L T*|
|* C-terminal amide ** C-terminal free acid|
Galanin is a peptide consisting of a chain of 29 amino acids (30 amino acids in humans) produced from the cleavage of a 123-amino acid protein known as prepro galanin, which is encoded by the GAL gene. The sequence of this gene is highly conserved among mammals, showing over 85% homology between rat, mouse, porcine, bovine, and human sequences. In these animal forms, the first 15 amino acids from the N-terminus are identical, but amino acids differ at several positions on the C-terminal end of the protein.
These slight differences in protein structure have far-reaching implications on their function. For example, porcine and rat galanin inhibit glucose-induced insulin secretion in rats and dogs but have no effect on insulin secretion in humans. This demonstrates that it is essential to study the effects of galanin and other regulatory peptides in their autologous species.
The galanin family of protein consists of four proteins, of which GAL was the first to be identified. The second was galanin message-associated protein (GMAP), a 59- or 60-amino acid peptide also formed from the cleavage of prepro galanin. The other two peptides, galanin-like peptide (GALP) and alarin, were identified relatively recently and are both encoded for in the same gene, the prepro GALP gene. GALP and alarin are produced by different post-transcriptional splicing of this gene.
Galanin signalling occurs through three classes of receptors, GALR1, GALR2, and GALR3, which are all part of the G protein-coupled receptor (GPCR) superfamily. Galanin receptors are expressed in the central nervous system, in the pancreas, and on solid tumours. The level of expression of the different receptors varies at each location, and this distribution changes after injury to neurons. Experiments into the function of the receptor subtypes involve mostly genetic knockout mice. The location of the receptor and the combination of receptors that are inhibited or stimulated heavily affect the outcome of galanin signalling.
One of the pathological features of the brain in the later stages of Alzheimer's disease is the presence of overgrown GAL-containing fibres innervating the surviving cholinergic neurons. Another feature is an increase in the expression of GAL and GAL receptors, in which increases of up to 200% have been observed in postmortem brains of Alzheimer's patients. The cause and role of this increase is poorly understood.
It has been suggested that the hyper-innervation acts to promote the death of these neurons and that the inhibitory effect of galanin on cholinergic neurons worsened the degeneration of cognitive function in patients by decreasing the amount of acetylcholine available to these neurons.
A second hypothesis has been generated based on data that suggest GAL is involved in protecting the hippocampus from excitotoxic damage and the neurons in the cholinergic basal forebrain from amyloid toxicity. It is interesting to note that studies of gene expression of CBF tissue suggests that the hyperinnervation of cholinergic neurons by GAL up regulates the transcription of factors that promote neuron function and survival. It is still unclear as to whether galanin acts to protect cholinergic neurons and promote their firing or whether it worsens the symptoms of this disease.
Galanin in the hippocampus is an inhibitor of glutamate but not of GABA. This means that galanin is capable of increasing the seizure threshold  and, therefore, is expected to act as an anticonvulsant. To be specific, GalR1 has been linked to the suppression of spontaneous seizures. An agonist antiepileptic drug candidate is NAX 5055.
It has been shown that galanin plays a role in the control of the early post-natal neural development of the dorsal root ganglion (DRG). Galanin-mutant animals show a 13% decrease in the number of adult DRG cells as well as a 24% decrease in the percentage of cells expressing substance P. This suggests that the cell loss by apoptosis that usually occurs in the developing DRG is regulated by galanin and that the absence of galanin results in an increase in the number of cells that die.
In vitro experiments show that DRG cells removed from galanin mutants have impaired abilities to extend neurites in culture, in that the number of cells producing neurites is decreased by a third and the mean length of these processes was halved when compared to wild-type controls. In vivo, many of the actions of galanin in the brain after an injury are similar to those observed in the developing DRG. Adult mutant animals have been shown to be 35% less capable of regenerating the sciatic nerve after crush injury, which is linked to long-term functional problems.
Parental role in mice
A report has indicated that Galanin-expressing neurons in the medial preoptic area of the brain are responsible for regulating aggression towards pups by male mice. 
- GRCh38: Ensembl release 89: ENSG00000069482 - Ensembl, May 2017
- GRCm38: Ensembl release 89: ENSMUSG00000024907 - Ensembl, May 2017
- "Human PubMed Reference:".
- "Mouse PubMed Reference:".
- Evans H, Baumgartner M, Shine J, Herzog H (December 1993). "Genomic organization and localization of the gene encoding human preprogalanin". Genomics. 18 (3): 473–7. doi:10.1016/S0888-7543(11)80002-9. PMID 7508413.
- Mitsukawa K, Lu X, Bartfai T (June 2008). "Galanin, galanin receptors and drug targets". Cell. Mol. Life Sci. 65 (12): 1796–805. doi:10.1007/s00018-008-8153-8. PMID 18500647.
- Mechenthaler I (June 2008). "Galanin and the neuroendocrine axes". Cell. Mol. Life Sci. 65 (12): 1826–35. doi:10.1007/s00018-008-8157-4. PMID 18500643.
- Wu Z, Autry AE, Bergan JF, Watabe-Uchida M, Dulac CG (May 2014). "Galanin neurons in the medial preoptic area govern parental behaviour". Nature. 509 (7500): 325–30. doi:10.1038/nature13307. PMC . PMID 24828191.
- Lundström L, Elmquist A, Bartfai T, Langel U (2005). "Galanin and its receptors in neurological disorders". Neuromolecular Med. 7 (1–2): 157–80. doi:10.1385/NMM:7:1-2:157. PMID 16052044.
- Berger A, Santic R, Hauser-Kronberger C, Schilling FH, Kogner P, Ratschek M, Gamper A, Jones N, Sperl W, Kofler B (June 2005). "Galanin and galanin receptors in human cancers". Neuropeptides. 39 (3): 353–9. doi:10.1016/j.npep.2004.12.016. PMID 15944034.
- Ito M (September 2009). "Functional roles of neuropeptides in cerebellar circuits". Neuroscience. 162 (3): 666–72. doi:10.1016/j.neuroscience.2009.01.019. PMID 19361475.
- Bartfai, T., (2000). "Galanin – A neuropeptide with important central nervous system actions". Archived from the original on December 2, 2010. Retrieved November 19, 2009.
- Wynick D, Thompson SW, McMahon SB (February 2001). "The role of galanin as a multi-functional neuropeptide in the nervous system". Current Opinion in Pharmacology. 1 (1): 73–7. doi:10.1016/S1471-4892(01)00006-6. PMID 11712539.
- Hökfelt T, Tatemoto K (June 2008). "Galanin--25 years with a multitalented neuropeptide". Cell. Mol. Life Sci. 65 (12): 1793–5. doi:10.1007/s00018-008-8152-9. PMID 18500648.
- Kaplan LM, Spindel ER, Isselbacher KJ, Chin WW (February 1988). "Tissue-specific expression of the rat galanin gene". Proc. Natl. Acad. Sci. U.S.A. 85 (4): 1065–9. doi:10.1073/pnas.85.4.1065. PMC . PMID 2448788.
- Bersani M, Johnsen AH, Højrup P, Dunning BE, Andreasen JJ, Holst JJ (June 1991). "Human galanin: primary structure and identification of two molecular forms". FEBS Lett. 283 (2): 189–94. doi:10.1016/0014-5793(91)80585-Q. PMID 1710578.
- Lang R, Gundlach AL, Kofler B (August 2007). "The galanin peptide family: receptor pharmacology, pleiotropic biological actions, and implications in health and disease". Pharmacol. Ther. 115 (2): 177–207. doi:10.1016/j.pharmthera.2007.05.009. PMID 17604107.
- Counts SE, Perez SE, Mufson EJ (June 2008). "Galanin in Alzheimer's disease: neuroinhibitory or neuroprotective?". Cell. Mol. Life Sci. 65 (12): 1842–53. doi:10.1007/s00018-008-8159-2. PMC . PMID 18500641.
- Counts SE, Perez SE, Ginsberg SD, De Lacalle S, Mufson EJ (May 2003). "Galanin in Alzheimer disease". Mol. Interv. 3 (3): 137–56. doi:10.1124/mi.3.3.137. PMID 14993421.
- Ding X, MacTavish D, Kar S, Jhamandas JH (February 2006). "Galanin attenuates beta-amyloid (Abeta) toxicity in rat cholinergic basal forebrain neurons". Neurobiol. Dis. 21 (2): 413–20. doi:10.1016/j.nbd.2005.08.016. PMID 16246567.
- Mazarati A, Lu X, Shinmei S, Badie-Mahdavi H, Bartfai T (2004). "Patterns of seizures, hippocampal injury and neurogenesis in three models of status epilepticus in galanin receptor type 1 (GalR1) knockout mice". Neuroscience. 128 (2): 431–41. doi:10.1016/j.neuroscience.2004.06.052. PMC . PMID 15350653.
- Zhang L, Robertson CR, Green BR, Pruess TH, White HS, Bulaj G (Mar 2009). "Structural requirements for a lipoamino acid in modulating the anticonvulsant activities of systemically active galanin analogues". Journal of Medicinal Chemistry. 52 (5): 1310–6. doi:10.1021/jm801397w. PMC . PMID 19199479.
- Bulaj G, Green BR, Lee HK, Robertson CR, White K, Zhang L, Sochanska M, Flynn SP, Scholl EA, Pruess TH, Smith MD, White HS (Dec 2008). "Design, synthesis, and characterization of high-affinity, systemically-active galanin analogues with potent anticonvulsant activities". Journal of Medicinal Chemistry. 51 (24): 8038–47. doi:10.1021/jm801088x. PMID 19053761.
- White HS, Scholl EA, Klein BD, Flynn SP, Pruess TH, Green BR, Zhang L, Bulaj G (Apr 2009). "Developing novel antiepileptic drugs: characterization of NAX 5055, a systemically-active galanin analog, in epilepsy models". Neurotherapeutics. 6 (2): 372–80. doi:10.1016/j.nurt.2009.01.001. PMC . PMID 19332332.
- Vrontakis ME (Dec 2002). "Galanin: a biologically active peptide". Current Drug Targets. CNS and Neurological Disorders. 1 (6): 531–41. doi:10.2174/1568007023338914. PMID 12769595.
- Mufson EJ, Counts SE, Perez SE, Binder L (Jun 2005). "Galanin plasticity in the cholinergic basal forebrain in Alzheimer's disease and transgenic mice". Neuropeptides. 39 (3): 233–7. doi:10.1016/j.npep.2004.12.005. PMID 15893372.
- Robinson JK, Bartfai T, Langel U (Jun 2006). "Galanin/GALP receptors and CNS homeostatic processes". CNS & Neurological Disorders Drug Targets. 5 (3): 327–34. doi:10.2174/187152706777452281. PMID 16787232.
- McKnight GL, Karlsen AE, Kowalyk S, Mathewes SL, Sheppard PO, O'Hara PJ, Taborsky GJ (Jan 1992). "Sequence of human galanin and its inhibition of glucose-stimulated insulin secretion from RIN cells". Diabetes. 41 (1): 82–7. doi:10.2337/diabetes.41.1.82. PMID 1370155.
- Gai WP, Geffen LB, Blessing WW (Aug 1990). "Galanin immunoreactive neurons in the human hypothalamus: colocalization with vasopressin-containing neurons". The Journal of Comparative Neurology. 298 (3): 265–80. doi:10.1002/cne.902980302. PMID 1698834.
- Burleigh DE, Furness JB (Jun 1990). "Distribution and actions of galanin and vasoactive intestinal peptide in the human colon". Neuropeptides. 16 (2): 77–82. doi:10.1016/0143-4179(90)90115-F. PMID 1701228.
- Fried G, Meister B, Rådestad A (Oct 1990). "Peptide-containing nerves in the human pregnant uterine cervix: an immunohistochemical study exploring the effect of RU 486 (mifepristone)". Human Reproduction. 5 (7): 870–6. PMID 1702449.
- Hyde JF, Engle MG, Maley BE (Jul 1991). "Colocalization of galanin and prolactin within secretory granules of anterior pituitary cells in estrogen-treated Fischer 344 rats". Endocrinology. 129 (1): 270–6. doi:10.1210/endo-129-1-270. PMID 1711463.
- Bennet WM, Hill SF, Ghatei MA, Bloom SR (Sep 1991). "Galanin in the normal human pituitary and brain and in pituitary adenomas". The Journal of Endocrinology. 130 (3): 463–7. doi:10.1677/joe.0.1300463. PMID 1719117.
- Schmidt WE, Kratzin H, Eckart K, Drevs D, Mundkowski G, Clemens A, Katsoulis S, Schäfer H, Gallwitz B, Creutzfeldt W (Dec 1991). "Isolation and primary structure of pituitary human galanin, a 30-residue nonamidated neuropeptide". Proceedings of the National Academy of Sciences of the United States of America. 88 (24): 11435–9. doi:10.1073/pnas.88.24.11435. PMC . PMID 1722333.
- Bauer FE, Christofides ND, Hacker GW, Blank MA, Polak JM, Bloom SR (1986). "Distribution of galanin immunoreactivity in the genitourinary tract of man and rat". Peptides. 7 (1): 5–10. doi:10.1016/0196-9781(86)90052-5. PMID 2423990.
- Bauer FE, Adrian TE, Christofides ND, Ferri GL, Yanaihara N, Polak JM, Bloom SR (Oct 1986). "Distribution and molecular heterogeneity of galanin in human, pig, guinea pig, and rat gastrointestinal tracts". Gastroenterology. 91 (4): 877–83. PMID 2427385.
- Tainio H, Vaalasti A, Rechardt L (1987). "The distribution of substance P-, CGRP-, galanin- and ANP-like immunoreactive nerves in human sweat glands". The Histochemical Journal. 19 (6–7): 375–80. doi:10.1007/BF01680455. PMID 2444569.
- Maggi CA, Santicioli P, Patacchini R, Turini D, Barbanti G, Beneforti P, Giuliani S, Meli A (Nov 1987). "Galanin: a potent modulator of excitatory neurotransmission in the human urinary bladder". European Journal of Pharmacology. 143 (1): 135–7. doi:10.1016/0014-2999(87)90744-8. PMID 2446889.
- Marti E, Gibson SJ, Polak JM, Facer P, Springall DR, Van Aswegen G, Aitchison M, Koltzenburg M (Dec 1987). "Ontogeny of peptide- and amine-containing neurones in motor, sensory, and autonomic regions of rat and human spinal cord, dorsal root ganglia, and rat skin". The Journal of Comparative Neurology. 266 (3): 332–59. doi:10.1002/cne.902660304. PMID 2447134.
- Beal MF, Clevens RA, Chattha GK, MacGarvey UM, Mazurek MF, Gabriel SM (Dec 1988). "Galanin-like immunoreactivity is unchanged in Alzheimer's disease and Parkinson's disease dementia cerebral cortex". Journal of Neurochemistry. 51 (6): 1935–41. doi:10.1111/j.1471-4159.1988.tb01181.x. PMID 2460590.
- Berrettini WH, Kaye WH, Sunderland T, May C, Gwirtsman HE, Mellow A, Albright A (1989). "Galanin immunoreactivity in human CSF: studies in eating disorders and Alzheimer's disease". Neuropsychobiology. 19 (2): 64–8. doi:10.1159/000118436. PMID 2465504.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Galanin message associated peptide (GMAP) Provide feedback
This family consists of several galanin message associated peptides. In rat preprogalanin, galanin is C-terminally flanked by a 60 amino acid long peptide: galanin message-associated peptide (GMAP). GMAP sequences in different species show high degree of homology, but the biological function of this family is unknown .
Andell-Jonsson S, Bartfai T; , Neuropeptides 1998;32:191-196.: Identification of the spinal degradation products and inhibition of adenylate cyclase by recombinant rat galanin message-associated peptide. PUBMED:9639260 EPMC:9639260
This tab holds annotation information from the InterPro database.
InterPro entry IPR013068
Galanin is a peptide hormone that controls various biological activities [PUBMED:1710578]. Galanin-like immuno-reactivity has been found in the central and peripheral nervous systems of mammals, with high concentrations demonstrated in discrete regions of the central nervous system, including the median eminence, hypothalamus, arcuate nucleus, septum, neuro-intermediate lobe of the pituitary, and the spinal cord. Its localisation within neurosecretory granules suggests that galanin may function as a neurotransmitter, and it has been shown to coexist with a variety of other peptide and amine neurotransmitters within individual neurons [PUBMED:2448788].
Although the precise physiological role of galanin is uncertain, it has a number of pharmacological properties: it stimulates food intake, when injected into the third ventricle of rats; it increases levels of plasma growth hormone and prolactin, and decreases dopamine levels in the median eminence [PUBMED:2448788]; and infusion into humans results in hyperglycemia and glucose intolerance, and inhibits pancreatic release of insulin, somatostatin and pancreatic peptide. Galanin also modulates smooth muscle contractility within the gastro-intestinal and genito-urinary tracts, all such activities suggesting that the hormone may play an important role in the nervous modulation of endocrine and smooth muscle function [PUBMED:2448788].
This domain represents the galanin message-associated peptide (GMAP) domain which is found C-terminal to the galanin domain in the preprogalanin precursor protein. GMAP sequences in different species show a high degree of homology, but the biological function of the GMAP peptide is not known [PUBMED:9639260].
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|Seed source:||Pfam-B_16759 (release 10.0)|
|Number in seed:||19|
|Number in full:||120|
|Average length of the domain:||56.00 aa|
|Average identity of full alignment:||54 %|
|Average coverage of the sequence by the domain:||40.60 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||11|
|Download:||download the raw HMM for this family|
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The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.