<p>Growth hormone, prolactin and somatolactin-family sequences were sought in diverse inver... more <p>Growth hormone, prolactin and somatolactin-family sequences were sought in diverse invertebrate genome and reference sequence databases using different available strategies. None of these search strategies could identify any putative invertebrate GH/PRL/SL homologs with the characteristic amino acid motif of the family, or indeed any significant sequence similarity. One sequence with high sequence identity to human PRL was identified from a tapeworm species; however this sequence is likely the result of horizontal gene transfer or contamination.</p> <p><strong>File information:</strong></p> <p><strong>In silico searches for putative growth hormone family homologs in invertebrates.pdf</strong><br>Description of methods and results, with references.</p> <p><strong>130723_Taenia_prl-hit_NJtree.phb</strong><br>Neighbor joining tree file in Newick format including the identified tapeworm sequence. Vertebrate species names are abbreviated to the first letter of the genus followed by the first two letters of the species (Hsa = Homo sapiens et. c.). The tapeworm sequence is identified with the UniProt ID Q8T110_9CEST.</p> <p><strong>130723_Taenia_prl-hit_NJtree.pdf</strong><br>Image of the neighbor joining tree (PDF). The tapeworm sequence is colored green.</p> <p><strong>Pairwise_align_hPRL+Taenia_prl-hit.txt</strong><br>Text file with the results of the pairwise alignment between the human PRL sequence and the identified tapeworm sequence.</p> <p><strong>HsaPRL+Taenia_prl-hit.aln</strong><br>Clustal alignment file containing the human PRL sequence and the identified tapeworm sequence.</p> <p> </p
Published in: Ocampo Daza D, Sundström G, Bergqvist CA, Larhammar D. The evolution of vertebrate ... more Published in: Ocampo Daza D, Sundström G, Bergqvist CA, Larhammar D. The evolution of vertebrate somatostatin receptors and their gene regions involves extensive chromosomal rearrangements. BMC Evolutionary Biology 2012, 12:231 doi:10.1186/1471-2148-12-231. Please refer to this article if using this figure. <strong>Figure 7 Continued from Figure 6.</strong> Paralogous chromosome regions in the stickleback and<br>zebrafish genomes. More rearrangements could be identified in the zebrafish genome than in<br>the stickleback or medaka genomes.
Sequence based phylogenetic analyses of 47 gene families identified in an analysis of conserved s... more Sequence based phylogenetic analyses of 47 gene families identified in an analysis of conserved synteny around somatostatin receptor gene-bearing chromosome regions. For each gene family amino acid sequences were predicted from the Ensembl genome browser (http://www.ensembl.org) and used to create sequence alignments and phylogenetic trees. Gene families were defined based on Ensembl protein family predictions. Database identifiers, location data, genome assembly information and annotation notes for all identified protein families and sequences are included in 'Supplemental Table 2.xlsx' and 'Supplemental Table 3.xlsx' (Excel spreadsheets). File information: Gene families are identified by unique abbreviations based on approved HUGO Gene Nomenclature Committe (HGNC) gene symbols, or known aliases from the NCBI Entrez Gene database. For each gene family an alignment file '...align.fasta', a neighbor joining tree '...NJ_rooted.phb' and a phylogenetic maximum likelihood tree '...PhyML_rooted.phb' are included. Alignments are included in FASTA format with the extension '.fasta'. This file format can be opened by most sequence analysis applications as well as text editors. Alignments were created using the ClustalWS sequence alignment program with standard settings (Gonnet weight matrix, gap opening penalty 10.0 and gap extension penalty 0.20) through the JABAWS 2 tool in Jalview 2.7 (http://www.jalview.org/). Phylogenetic tree files are included in Phylip/Newick format with the extension '.phb'. This file format can be opened by freely available phylogenetic tree viewers such as FigTree (http://tree.bio.ed.ac.uk/software/figtree/) and TreeView (http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/). The phylogenetic analyses were carried out based on the included alignments using bootstrap-supported neighbor joining (NJ) as well as phylogenetic maximum likelihood (PhyML) methods. Phylogenetic trees are rooted with identified <em>Drosophila melanogaster </em>(fruit fly) sequences, or with identified <em>Ciona intestina [...]
The neuropeptide Y system is known to have expanded in early vertebrate evolution. Three neuropep... more The neuropeptide Y system is known to have expanded in early vertebrate evolution. Three neuropeptide Y receptors have been proposed to have existed before the two basal vertebrate tetraploidizations, namely a Y1-like, a Y2-like, and a Y5-like receptor, with their genes in the same chromosomal region. Previously we have described a Y1-subfamily and a Y2-subfamily receptor in the river lamprey, Lampetra fluviatilis. Here we report the identification of a Y5 receptor in the genome of the sea lamprey, Petromyzon marinus. In phylogenetic analyses, the Y5 receptor clusters together with gnathostome Y5 receptors with high bootstrap value and shares the long intracellular loop 3. This lamprey receptor has an even longer loop 3 than the gnathostome Y5 receptors described so far, with the expansion of amino acid repeats. Functional expression in a human cell line, co-transfected with a modified human G-protein, resulted in inositol phosphate turnover in response to the three lamprey NPY-family peptides NPY, PYY and PMY at nanomolar concentrations. Our results confirm that the Y1-Y2-Y5 receptor gene triplet arose before the cyclostome-gnathostome divergence. However, it is not clear from the NPY receptors whether cyclostomes diverged from the gnathostome lineage after the first or the second tetraploidization. Duplicates resulting from the tetraploidizations exist for both Y1 and Y2 in gnathostomes, but only a single copy of Y5 has survived in all vertebrates characterized to date, making the physiological roles of Y5 interesting to explore.
The ancestor of gnathostomes (jawed vertebrates) is generally considered to have undergone two ro... more The ancestor of gnathostomes (jawed vertebrates) is generally considered to have undergone two rounds of whole genome duplication (WGD). The timing of these WGD events relative to the divergence of the closest relatives of the gnathostomes, the cyclostomes, has remained contentious. Lampreys and hagfishes are extant cyclostomes whose gene families can shed light on the relationship between the WGDs and the cyclostome-gnathostome divergence. Previously, we have characterized in detail the evolution of the gnathostome corticotropin-releasing hormone (CRH) family and found that its five members arose from two ancestral genes that existed before the WGDs. The two WGDs resulted, after secondary losses, in one triplet consisting of CRH1, CRH2, and UCN1, and one pair consisting of UCN2 and UCN3. All five genes exist in representatives for cartilaginous fishes, ray-finned fishes, and lobe-finned fishes. Differential losses have occurred in some lineages. We present here analyses of CRH-family members in lamprey and hagfish by comparing sequences and gene synteny with gnathostomes. We found five CRH-family genes in each of two lamprey species (Petromyzon marinus and Lethenteron camtschaticum) and two genes in a hagfish (Eptatretus burgeri). Synteny analyses show that all five lamprey CRH-family genes have similar chromosomal neighbors as the gnathostome genes. The most parsimonious explanation is that the lamprey CRH-family genes are orthologs of the five gnathostome genes and thus arose in the same chromosome duplications. This suggests that lampreys and gnathostomes share the same two WGD events and that these took place before the lamprey-gnathostome divergence.
Neuropeptide F (NPF), the invertebrate homolog of neuropeptide Y (NPY) in vertebrates, shares sim... more Neuropeptide F (NPF), the invertebrate homolog of neuropeptide Y (NPY) in vertebrates, shares similarity of structure and function with NPY. However, a few NPYs were also found in some insect species. In this paper, two neuropeptide genes encoding a NPF and a NPY were cloned from a tobacco budworm Helicoverpa assulta cDNA library. The npf1 gene further produces two splicing variants of rnRNAs, i.e. npf1a (lacks the 120 bp segment) and npf1b (includes a 120 bp segment). These two splicing variants form two mature peptides, NPF1a and NPF1b by modification of transcripts. NPF and NPY co-exist in H. assulta.
The genes of the polymorphic HLA-DR molecules are located within the human major histocompatibili... more The genes of the polymorphic HLA-DR molecules are located within the human major histocompatibility complex. We have studied the HLA-DR genes of an HLA homozygous individual typed to be DR4, Dw4, and DRw53. Fourteen cosmid and phage clones from genomic libraries were isolated and grouped into three clusters comprising a total of 165 kilobases. These clusters contain four DR beta genes. Nucleotide sequence determination showed that two of the genes encode beta chains that carry the DR4 and DRw53 specificities, respectively, while the other two genes are presumably pseudogenes. Comparisons of the nucleotide sequences of all four DR beta genes of the DR4 haplotype show that the genes are extensively similar, approximately 90% in both exons and introns. All four genes are equally similar to each other. These observations are consistent with the notion that the genes arose by duplications that were followed by homogenization through gene conversion. The existence of more than one DR beta gene homologue but only a single DR alpha gene homologue in mouse, rabbit, and cattle suggests that the DR beta gene duplications occurred at or early during mammalian speciation.
bioRxiv (Cold Spring Harbor Laboratory), Sep 19, 2022
Cyclic nucleotide-gated (CNG) cation channels are important heterotetrameric proteins in the reti... more Cyclic nucleotide-gated (CNG) cation channels are important heterotetrameric proteins in the retina, with different subunit composition in cone and rod photoreceptor cells: three CNGA3 and one CNGB3 in cones and three CNGA1 and one CNGB1 in rods. CNGA and CNGB subunits form separate subfamilies. We have analyzed the evolution of the CNG gene family in metazoans, with special focus on vertebrates by using sequence-based phylogeny and conservation of chromosomal synteny to deduce paralogons resulting from the early vertebrate whole genome duplications (WGDs). Our analyses show, unexpectedly, that the CNGA subfamily had four sister subfamilies in the ancestor of bilaterians and cnidarians that we named CNGC, CNGD, CNGE and CNGF. Of these, CNGC, CNGE and CNGF were lost in the ancestor of Olfactores while CNGD was lost in the vertebrate ancestor. The remaining CNGA and CNGB genes were expanded by a local duplication of CNGA and the subsequent chromosome duplications in the basal vertebrate WGD events. Upon some losses, this resulted in the gnathostome ancestor having three members in the visual CNGA subfamily (CNGA1-3), a single CNGA4 gene, and two members in the CNGB subfamily (CNGB1 and CNGB3). The nature of chromosomal rearrangements in the vertebrate CNGA paralogon was resolved by including the genomes of a non-teleost actinopterygian and an elasmobranch. After the teleost-specific WGD, additional duplicates were generated and retained for CNGA1, CNGA2, CNGA3 and CNGB1. Furthermore, teleosts retain a local duplicate of CNGB3. The retention of duplicated CNG genes is explained by their subfunctionalisation and photoreceptor-specific expression. In conclusion, this study provides evidence for four previously unknown CNG subfamilies in invertebrates and further evidence that the early vertebrate WGD events were instrumental in the evolution of the vertebrate visual and central nervous systems. .
Journal of Pharmacology and Experimental Therapeutics, Nov 26, 2019
Itch stimuli are detected by specialized primary afferents that convey the signal to the spinal c... more Itch stimuli are detected by specialized primary afferents that convey the signal to the spinal cord, but how itch transmission is regulated is still not completely known. Here, we investigated the roles of the neuropeptide Y (NPY)/Y 2 receptor system on scratch behavior. The inhibitory Y 2 receptor is expressed on mouse primary afferents, and intrathecal administration of the Y 2 agonist peptide YY (PYY) 3-36 reduced scratch episode frequency and duration induced by compound 48/80, an effect that could be reversed by intrathecal preadministration of the Y 2 antagonist BIIE0246. Also, scratch episode duration induced by histamine could be reduced by PYY 3-36. In contrast, scratch behavior induced by a-methyl-5HT, protease-activated receptor-2-activating peptide SLIGRL, chloroquine, topical dust mite extract, or mechanical itch induced by von Frey filaments was unaffected by stimulation of Y 2. Primary afferent neurons expressing the Npy2r gene were found to coexpress itch-associated markers such as natriuretic peptide precursor b, oncostatin M receptor, and interleukin (IL) 31 receptor A. Accordingly, intrathecal PYY 3-36 reduced the scratch behavior induced by IL-31. Our findings imply that the NPY/Y 2 system reduces histaminergic and IL-31-associated itch through presynaptic inhibition of a subpopulation of itch-associated primary afferents. SIGNIFICANCE STATEMENT The spinal neuropeptide Y system dampens scratching behavior induced by histaminergic compounds and interleukin 31, a cytokine involved in atopic dermatitis, through interactions with the Y 2 receptor. The Y 2 receptor is expressed by primary afferent neurons that are rich in itch-associated neurotransmitters and receptors such as somatostatin, natriuretic peptide precursor b, and interleukin 31 receptors.
General and Comparative Endocrinology, Aug 1, 2018
Highlights • PRL and PRL2 genes arose in the basal vertebrate tetraploidizations (1R and 2R). • S... more Highlights • PRL and PRL2 genes arose in the basal vertebrate tetraploidizations (1R and 2R). • SL duplicated in teleost tetraploidization (3R) producing SLa and SLb. • GH, PRL/PRL2 and SL genes were present already before the vertebrate radiation. • Genomic evidence suggests origin of family through local duplications before 1R/2R.
The genes of the polymorphic HLA-DR molecules are located within the human major histocompatibili... more The genes of the polymorphic HLA-DR molecules are located within the human major histocompatibility complex. We have studied the HLA-DR genes of an HLA homozygous individual typed to be DR4, Dw4, and DRw53. Fourteen cosmid and phage clones from genomic libraries were isolated and grouped into three clusters comprising a total of 165 kilobases. These clusters contain four DR beta genes. Nucleotide sequence determination showed that two of the genes encode beta chains that carry the DR4 and DRw53 specificities, respectively, while the other two genes are presumably pseudogenes. Comparisons of the nucleotide sequences of all four DR beta genes of the DR4 haplotype show that the genes are extensively similar, approximately 90% in both exons and introns. All four genes are equally similar to each other. These observations are consistent with the notion that the genes arose by duplications that were followed by homogenization through gene conversion. The existence of more than one DR beta gene homologue but only a single DR alpha gene homologue in mouse, rabbit, and cattle suggests that the DR beta gene duplications occurred at or early during mammalian speciation.
A correlation is known to exist between visual sensitivity and oscillations in red opsin and rhod... more A correlation is known to exist between visual sensitivity and oscillations in red opsin and rhodopsin gene expression in zebrafish, both regulated by the clock gene. This indicates that an endogenous circadian clock regulates behavioural visual sensitivity, apart from the regulation exerted by the pineal organ. However, the specific mechanisms for cones (photopic vision) and rods (scotopic vision) are poorly understood. In this work, we performed gene expression, cosinor and immunohistochemical analyses to investigate other key genes involved in light perception, encoding the different subunits of phosphodiesterase pde6 and transducin Gα T , in constant lighting conditions and compared to normal light-dark conditions. We found that cones display prominent circadian oscillations in mRNA levels for the inhibitory subunit gene pde6ha that could contribute to the regulation of photopic sensitivity by preventing overstimulation in photopic conditions. In rods, the mRNA levels of the inhibitory subunit gene pde6ga oscillate under normal conditions and dampen down in constant light but continue oscillating in constant darkness. There is an increase in total relative expression for pde6gb in constant conditions. These observations, together with previous data, suggest a complex regulation of the scotopic sensitivity involving endogenous and non-endogenous components, possibly present also in other teleost species. The Gα T genes do not display mRNA oscillations and therefore may not be essential for the circadian regulation of photosensitivity. In summary, our results support different regulation for the zebrafish photopic and scotopic sensitivities and suggest circadian regulation of pde6ha as a key factor regulating photopic sensitivity, while the regulatory mechanisms in rods appear to be more complex.
The evolution of the IGF binding protein (IGFBP) gene family has been difficult to resolve. Both ... more The evolution of the IGF binding protein (IGFBP) gene family has been difficult to resolve. Both chromosomal and serial duplications have been suggested as mechanisms for the expansion of this gene family. We have identified and annotated IGFBP sequences from a wide selection of vertebrate species as well as Branchiostoma floridae and Ciona intestinalis. By combining detailed sequence analysis with sequence-based phylogenies and chromosome information, we arrive at the following scenario: the ancestral chordate IGFBP gene underwent a local gene duplication, resulting in a gene pair adjacent to a HOX cluster. Subsequently, the gene family expanded in the two basal vertebrate tetraploidization (2R) resulting in the six IGFBP types that are presently found in placental mammals. The teleost fish ancestor underwent a third tetraploidization (3R) that further expanded the IGFBP repertoire. The five sequenced teleost fish genomes retain 9-11 of IGFBP genes. This scenario is supported by the phylogenies of three adjacent gene families in the HOX gene regions, namely the epidermal growth factor receptors (EGFR) and the Ikaros and distal-less (DLX) transcription factors. Our sequence comparisons show that several important structural components in the IGFBPs are ancestral vertebrate features that have been maintained in all orthologs, for instance the integrin interaction motif Arg-Gly-Asp in IGFBP-2. In contrast, the Arg-Gly-Asp motif in IGFBP-1 has arisen independently in mammals. The large degree of retention of IGFBP genes after the ancient expansion of the gene family strongly suggests that each gene evolved distinct and important functions early in vertebrate evolution.
The genes of the polymorphic HLA-DR molecules are located within the human major histocompatibili... more The genes of the polymorphic HLA-DR molecules are located within the human major histocompatibility complex. We have studied the HLA-DR genes of an HLA homozygous individual typed to be DR4, Dw4, and DRw53. Fourteen cosmid and phage clones from genomic libraries were isolated and grouped into three clusters comprising a total of 165 kilobases. These clusters contain four DR beta genes. Nucleotide sequence determination showed that two of the genes encode beta chains that carry the DR4 and DRw53 specificities, respectively, while the other two genes are presumably pseudogenes. Comparisons of the nucleotide sequences of all four DR beta genes of the DR4 haplotype show that the genes are extensively similar, approximately 90% in both exons and introns. All four genes are equally similar to each other. These observations are consistent with the notion that the genes arose by duplications that were followed by homogenization through gene conversion. The existence of more than one DR beta gene homologue but only a single DR alpha gene homologue in mouse, rabbit, and cattle suggests that the DR beta gene duplications occurred at or early during mammalian speciation.
<p>Growth hormone, prolactin and somatolactin-family sequences were sought in diverse inver... more <p>Growth hormone, prolactin and somatolactin-family sequences were sought in diverse invertebrate genome and reference sequence databases using different available strategies. None of these search strategies could identify any putative invertebrate GH/PRL/SL homologs with the characteristic amino acid motif of the family, or indeed any significant sequence similarity. One sequence with high sequence identity to human PRL was identified from a tapeworm species; however this sequence is likely the result of horizontal gene transfer or contamination.</p> <p><strong>File information:</strong></p> <p><strong>In silico searches for putative growth hormone family homologs in invertebrates.pdf</strong><br>Description of methods and results, with references.</p> <p><strong>130723_Taenia_prl-hit_NJtree.phb</strong><br>Neighbor joining tree file in Newick format including the identified tapeworm sequence. Vertebrate species names are abbreviated to the first letter of the genus followed by the first two letters of the species (Hsa = Homo sapiens et. c.). The tapeworm sequence is identified with the UniProt ID Q8T110_9CEST.</p> <p><strong>130723_Taenia_prl-hit_NJtree.pdf</strong><br>Image of the neighbor joining tree (PDF). The tapeworm sequence is colored green.</p> <p><strong>Pairwise_align_hPRL+Taenia_prl-hit.txt</strong><br>Text file with the results of the pairwise alignment between the human PRL sequence and the identified tapeworm sequence.</p> <p><strong>HsaPRL+Taenia_prl-hit.aln</strong><br>Clustal alignment file containing the human PRL sequence and the identified tapeworm sequence.</p> <p> </p
Published in: Ocampo Daza D, Sundström G, Bergqvist CA, Larhammar D. The evolution of vertebrate ... more Published in: Ocampo Daza D, Sundström G, Bergqvist CA, Larhammar D. The evolution of vertebrate somatostatin receptors and their gene regions involves extensive chromosomal rearrangements. BMC Evolutionary Biology 2012, 12:231 doi:10.1186/1471-2148-12-231. Please refer to this article if using this figure. <strong>Figure 7 Continued from Figure 6.</strong> Paralogous chromosome regions in the stickleback and<br>zebrafish genomes. More rearrangements could be identified in the zebrafish genome than in<br>the stickleback or medaka genomes.
Sequence based phylogenetic analyses of 47 gene families identified in an analysis of conserved s... more Sequence based phylogenetic analyses of 47 gene families identified in an analysis of conserved synteny around somatostatin receptor gene-bearing chromosome regions. For each gene family amino acid sequences were predicted from the Ensembl genome browser (http://www.ensembl.org) and used to create sequence alignments and phylogenetic trees. Gene families were defined based on Ensembl protein family predictions. Database identifiers, location data, genome assembly information and annotation notes for all identified protein families and sequences are included in 'Supplemental Table 2.xlsx' and 'Supplemental Table 3.xlsx' (Excel spreadsheets). File information: Gene families are identified by unique abbreviations based on approved HUGO Gene Nomenclature Committe (HGNC) gene symbols, or known aliases from the NCBI Entrez Gene database. For each gene family an alignment file '...align.fasta', a neighbor joining tree '...NJ_rooted.phb' and a phylogenetic maximum likelihood tree '...PhyML_rooted.phb' are included. Alignments are included in FASTA format with the extension '.fasta'. This file format can be opened by most sequence analysis applications as well as text editors. Alignments were created using the ClustalWS sequence alignment program with standard settings (Gonnet weight matrix, gap opening penalty 10.0 and gap extension penalty 0.20) through the JABAWS 2 tool in Jalview 2.7 (http://www.jalview.org/). Phylogenetic tree files are included in Phylip/Newick format with the extension '.phb'. This file format can be opened by freely available phylogenetic tree viewers such as FigTree (http://tree.bio.ed.ac.uk/software/figtree/) and TreeView (http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/). The phylogenetic analyses were carried out based on the included alignments using bootstrap-supported neighbor joining (NJ) as well as phylogenetic maximum likelihood (PhyML) methods. Phylogenetic trees are rooted with identified <em>Drosophila melanogaster </em>(fruit fly) sequences, or with identified <em>Ciona intestina [...]
The neuropeptide Y system is known to have expanded in early vertebrate evolution. Three neuropep... more The neuropeptide Y system is known to have expanded in early vertebrate evolution. Three neuropeptide Y receptors have been proposed to have existed before the two basal vertebrate tetraploidizations, namely a Y1-like, a Y2-like, and a Y5-like receptor, with their genes in the same chromosomal region. Previously we have described a Y1-subfamily and a Y2-subfamily receptor in the river lamprey, Lampetra fluviatilis. Here we report the identification of a Y5 receptor in the genome of the sea lamprey, Petromyzon marinus. In phylogenetic analyses, the Y5 receptor clusters together with gnathostome Y5 receptors with high bootstrap value and shares the long intracellular loop 3. This lamprey receptor has an even longer loop 3 than the gnathostome Y5 receptors described so far, with the expansion of amino acid repeats. Functional expression in a human cell line, co-transfected with a modified human G-protein, resulted in inositol phosphate turnover in response to the three lamprey NPY-family peptides NPY, PYY and PMY at nanomolar concentrations. Our results confirm that the Y1-Y2-Y5 receptor gene triplet arose before the cyclostome-gnathostome divergence. However, it is not clear from the NPY receptors whether cyclostomes diverged from the gnathostome lineage after the first or the second tetraploidization. Duplicates resulting from the tetraploidizations exist for both Y1 and Y2 in gnathostomes, but only a single copy of Y5 has survived in all vertebrates characterized to date, making the physiological roles of Y5 interesting to explore.
The ancestor of gnathostomes (jawed vertebrates) is generally considered to have undergone two ro... more The ancestor of gnathostomes (jawed vertebrates) is generally considered to have undergone two rounds of whole genome duplication (WGD). The timing of these WGD events relative to the divergence of the closest relatives of the gnathostomes, the cyclostomes, has remained contentious. Lampreys and hagfishes are extant cyclostomes whose gene families can shed light on the relationship between the WGDs and the cyclostome-gnathostome divergence. Previously, we have characterized in detail the evolution of the gnathostome corticotropin-releasing hormone (CRH) family and found that its five members arose from two ancestral genes that existed before the WGDs. The two WGDs resulted, after secondary losses, in one triplet consisting of CRH1, CRH2, and UCN1, and one pair consisting of UCN2 and UCN3. All five genes exist in representatives for cartilaginous fishes, ray-finned fishes, and lobe-finned fishes. Differential losses have occurred in some lineages. We present here analyses of CRH-family members in lamprey and hagfish by comparing sequences and gene synteny with gnathostomes. We found five CRH-family genes in each of two lamprey species (Petromyzon marinus and Lethenteron camtschaticum) and two genes in a hagfish (Eptatretus burgeri). Synteny analyses show that all five lamprey CRH-family genes have similar chromosomal neighbors as the gnathostome genes. The most parsimonious explanation is that the lamprey CRH-family genes are orthologs of the five gnathostome genes and thus arose in the same chromosome duplications. This suggests that lampreys and gnathostomes share the same two WGD events and that these took place before the lamprey-gnathostome divergence.
Neuropeptide F (NPF), the invertebrate homolog of neuropeptide Y (NPY) in vertebrates, shares sim... more Neuropeptide F (NPF), the invertebrate homolog of neuropeptide Y (NPY) in vertebrates, shares similarity of structure and function with NPY. However, a few NPYs were also found in some insect species. In this paper, two neuropeptide genes encoding a NPF and a NPY were cloned from a tobacco budworm Helicoverpa assulta cDNA library. The npf1 gene further produces two splicing variants of rnRNAs, i.e. npf1a (lacks the 120 bp segment) and npf1b (includes a 120 bp segment). These two splicing variants form two mature peptides, NPF1a and NPF1b by modification of transcripts. NPF and NPY co-exist in H. assulta.
The genes of the polymorphic HLA-DR molecules are located within the human major histocompatibili... more The genes of the polymorphic HLA-DR molecules are located within the human major histocompatibility complex. We have studied the HLA-DR genes of an HLA homozygous individual typed to be DR4, Dw4, and DRw53. Fourteen cosmid and phage clones from genomic libraries were isolated and grouped into three clusters comprising a total of 165 kilobases. These clusters contain four DR beta genes. Nucleotide sequence determination showed that two of the genes encode beta chains that carry the DR4 and DRw53 specificities, respectively, while the other two genes are presumably pseudogenes. Comparisons of the nucleotide sequences of all four DR beta genes of the DR4 haplotype show that the genes are extensively similar, approximately 90% in both exons and introns. All four genes are equally similar to each other. These observations are consistent with the notion that the genes arose by duplications that were followed by homogenization through gene conversion. The existence of more than one DR beta gene homologue but only a single DR alpha gene homologue in mouse, rabbit, and cattle suggests that the DR beta gene duplications occurred at or early during mammalian speciation.
bioRxiv (Cold Spring Harbor Laboratory), Sep 19, 2022
Cyclic nucleotide-gated (CNG) cation channels are important heterotetrameric proteins in the reti... more Cyclic nucleotide-gated (CNG) cation channels are important heterotetrameric proteins in the retina, with different subunit composition in cone and rod photoreceptor cells: three CNGA3 and one CNGB3 in cones and three CNGA1 and one CNGB1 in rods. CNGA and CNGB subunits form separate subfamilies. We have analyzed the evolution of the CNG gene family in metazoans, with special focus on vertebrates by using sequence-based phylogeny and conservation of chromosomal synteny to deduce paralogons resulting from the early vertebrate whole genome duplications (WGDs). Our analyses show, unexpectedly, that the CNGA subfamily had four sister subfamilies in the ancestor of bilaterians and cnidarians that we named CNGC, CNGD, CNGE and CNGF. Of these, CNGC, CNGE and CNGF were lost in the ancestor of Olfactores while CNGD was lost in the vertebrate ancestor. The remaining CNGA and CNGB genes were expanded by a local duplication of CNGA and the subsequent chromosome duplications in the basal vertebrate WGD events. Upon some losses, this resulted in the gnathostome ancestor having three members in the visual CNGA subfamily (CNGA1-3), a single CNGA4 gene, and two members in the CNGB subfamily (CNGB1 and CNGB3). The nature of chromosomal rearrangements in the vertebrate CNGA paralogon was resolved by including the genomes of a non-teleost actinopterygian and an elasmobranch. After the teleost-specific WGD, additional duplicates were generated and retained for CNGA1, CNGA2, CNGA3 and CNGB1. Furthermore, teleosts retain a local duplicate of CNGB3. The retention of duplicated CNG genes is explained by their subfunctionalisation and photoreceptor-specific expression. In conclusion, this study provides evidence for four previously unknown CNG subfamilies in invertebrates and further evidence that the early vertebrate WGD events were instrumental in the evolution of the vertebrate visual and central nervous systems. .
Journal of Pharmacology and Experimental Therapeutics, Nov 26, 2019
Itch stimuli are detected by specialized primary afferents that convey the signal to the spinal c... more Itch stimuli are detected by specialized primary afferents that convey the signal to the spinal cord, but how itch transmission is regulated is still not completely known. Here, we investigated the roles of the neuropeptide Y (NPY)/Y 2 receptor system on scratch behavior. The inhibitory Y 2 receptor is expressed on mouse primary afferents, and intrathecal administration of the Y 2 agonist peptide YY (PYY) 3-36 reduced scratch episode frequency and duration induced by compound 48/80, an effect that could be reversed by intrathecal preadministration of the Y 2 antagonist BIIE0246. Also, scratch episode duration induced by histamine could be reduced by PYY 3-36. In contrast, scratch behavior induced by a-methyl-5HT, protease-activated receptor-2-activating peptide SLIGRL, chloroquine, topical dust mite extract, or mechanical itch induced by von Frey filaments was unaffected by stimulation of Y 2. Primary afferent neurons expressing the Npy2r gene were found to coexpress itch-associated markers such as natriuretic peptide precursor b, oncostatin M receptor, and interleukin (IL) 31 receptor A. Accordingly, intrathecal PYY 3-36 reduced the scratch behavior induced by IL-31. Our findings imply that the NPY/Y 2 system reduces histaminergic and IL-31-associated itch through presynaptic inhibition of a subpopulation of itch-associated primary afferents. SIGNIFICANCE STATEMENT The spinal neuropeptide Y system dampens scratching behavior induced by histaminergic compounds and interleukin 31, a cytokine involved in atopic dermatitis, through interactions with the Y 2 receptor. The Y 2 receptor is expressed by primary afferent neurons that are rich in itch-associated neurotransmitters and receptors such as somatostatin, natriuretic peptide precursor b, and interleukin 31 receptors.
General and Comparative Endocrinology, Aug 1, 2018
Highlights • PRL and PRL2 genes arose in the basal vertebrate tetraploidizations (1R and 2R). • S... more Highlights • PRL and PRL2 genes arose in the basal vertebrate tetraploidizations (1R and 2R). • SL duplicated in teleost tetraploidization (3R) producing SLa and SLb. • GH, PRL/PRL2 and SL genes were present already before the vertebrate radiation. • Genomic evidence suggests origin of family through local duplications before 1R/2R.
The genes of the polymorphic HLA-DR molecules are located within the human major histocompatibili... more The genes of the polymorphic HLA-DR molecules are located within the human major histocompatibility complex. We have studied the HLA-DR genes of an HLA homozygous individual typed to be DR4, Dw4, and DRw53. Fourteen cosmid and phage clones from genomic libraries were isolated and grouped into three clusters comprising a total of 165 kilobases. These clusters contain four DR beta genes. Nucleotide sequence determination showed that two of the genes encode beta chains that carry the DR4 and DRw53 specificities, respectively, while the other two genes are presumably pseudogenes. Comparisons of the nucleotide sequences of all four DR beta genes of the DR4 haplotype show that the genes are extensively similar, approximately 90% in both exons and introns. All four genes are equally similar to each other. These observations are consistent with the notion that the genes arose by duplications that were followed by homogenization through gene conversion. The existence of more than one DR beta gene homologue but only a single DR alpha gene homologue in mouse, rabbit, and cattle suggests that the DR beta gene duplications occurred at or early during mammalian speciation.
A correlation is known to exist between visual sensitivity and oscillations in red opsin and rhod... more A correlation is known to exist between visual sensitivity and oscillations in red opsin and rhodopsin gene expression in zebrafish, both regulated by the clock gene. This indicates that an endogenous circadian clock regulates behavioural visual sensitivity, apart from the regulation exerted by the pineal organ. However, the specific mechanisms for cones (photopic vision) and rods (scotopic vision) are poorly understood. In this work, we performed gene expression, cosinor and immunohistochemical analyses to investigate other key genes involved in light perception, encoding the different subunits of phosphodiesterase pde6 and transducin Gα T , in constant lighting conditions and compared to normal light-dark conditions. We found that cones display prominent circadian oscillations in mRNA levels for the inhibitory subunit gene pde6ha that could contribute to the regulation of photopic sensitivity by preventing overstimulation in photopic conditions. In rods, the mRNA levels of the inhibitory subunit gene pde6ga oscillate under normal conditions and dampen down in constant light but continue oscillating in constant darkness. There is an increase in total relative expression for pde6gb in constant conditions. These observations, together with previous data, suggest a complex regulation of the scotopic sensitivity involving endogenous and non-endogenous components, possibly present also in other teleost species. The Gα T genes do not display mRNA oscillations and therefore may not be essential for the circadian regulation of photosensitivity. In summary, our results support different regulation for the zebrafish photopic and scotopic sensitivities and suggest circadian regulation of pde6ha as a key factor regulating photopic sensitivity, while the regulatory mechanisms in rods appear to be more complex.
The evolution of the IGF binding protein (IGFBP) gene family has been difficult to resolve. Both ... more The evolution of the IGF binding protein (IGFBP) gene family has been difficult to resolve. Both chromosomal and serial duplications have been suggested as mechanisms for the expansion of this gene family. We have identified and annotated IGFBP sequences from a wide selection of vertebrate species as well as Branchiostoma floridae and Ciona intestinalis. By combining detailed sequence analysis with sequence-based phylogenies and chromosome information, we arrive at the following scenario: the ancestral chordate IGFBP gene underwent a local gene duplication, resulting in a gene pair adjacent to a HOX cluster. Subsequently, the gene family expanded in the two basal vertebrate tetraploidization (2R) resulting in the six IGFBP types that are presently found in placental mammals. The teleost fish ancestor underwent a third tetraploidization (3R) that further expanded the IGFBP repertoire. The five sequenced teleost fish genomes retain 9-11 of IGFBP genes. This scenario is supported by the phylogenies of three adjacent gene families in the HOX gene regions, namely the epidermal growth factor receptors (EGFR) and the Ikaros and distal-less (DLX) transcription factors. Our sequence comparisons show that several important structural components in the IGFBPs are ancestral vertebrate features that have been maintained in all orthologs, for instance the integrin interaction motif Arg-Gly-Asp in IGFBP-2. In contrast, the Arg-Gly-Asp motif in IGFBP-1 has arisen independently in mammals. The large degree of retention of IGFBP genes after the ancient expansion of the gene family strongly suggests that each gene evolved distinct and important functions early in vertebrate evolution.
The genes of the polymorphic HLA-DR molecules are located within the human major histocompatibili... more The genes of the polymorphic HLA-DR molecules are located within the human major histocompatibility complex. We have studied the HLA-DR genes of an HLA homozygous individual typed to be DR4, Dw4, and DRw53. Fourteen cosmid and phage clones from genomic libraries were isolated and grouped into three clusters comprising a total of 165 kilobases. These clusters contain four DR beta genes. Nucleotide sequence determination showed that two of the genes encode beta chains that carry the DR4 and DRw53 specificities, respectively, while the other two genes are presumably pseudogenes. Comparisons of the nucleotide sequences of all four DR beta genes of the DR4 haplotype show that the genes are extensively similar, approximately 90% in both exons and introns. All four genes are equally similar to each other. These observations are consistent with the notion that the genes arose by duplications that were followed by homogenization through gene conversion. The existence of more than one DR beta gene homologue but only a single DR alpha gene homologue in mouse, rabbit, and cattle suggests that the DR beta gene duplications occurred at or early during mammalian speciation.
Uploads
Papers by Dan Larhammar