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  • 1.
    Björk, Petra
    et al.
    Stockholm University.
    Baurén, Göran
    Stockholm University.
    Jin, ShaoBo
    Stockholm University.
    Tong, Yong-Guang
    Karolinska Institutet.
    Bürglin, Thomas R.
    Karolinska Institutet.
    Hellman, Ulf
    Ludwig Institute for Cancer Research.
    Wieslander, Lars
    Stockholm University.
    A novel conserved RNA-binding domain protein, RBD-1, is essential for ribosome biogenesis2002Inngår i: Molecular Biology of the Cell, ISSN 1059-1524, E-ISSN 1939-4586, Vol. 13, nr 10, s. 3683-3695Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Synthesis of the ribosomal subunits from pre-rRNA requires a large number of trans-acting proteins and small nucleolar ribonucleoprotein particles to execute base modifications, RNA cleavages, and structural rearrangements. We have characterized a novel protein, RNA-binding domain-1 (RBD-1), that is involved in ribosome biogenesis. This protein contains six consensus RNA-binding domains and is conserved as to sequence, domain organization, and cellular location from yeast to human. RBD-1 is essential in Caenorhabditis elegans. In the dipteran Chironomus tentans, RBD-1 (Ct-RBD-1) binds pre-rRNA in vitro and anti-Ct-RBD-1 antibodies repress pre-rRNA processing in vivo. Ct-RBD-1 is mainly located in the nucleolus in an RNA polymerase I transcription-dependent manner, but it is also present in discrete foci in the interchromatin and in the cytoplasm. In cytoplasmic extracts, 20-30% of Ct-RBD-1 is associated with ribosomes and, preferentially, with the 40S ribosomal subunit. Our data suggest that RBD-1 plays a role in structurally coordinating pre-rRNA during ribosome biogenesis and that this function is conserved in all eukaryotes.

  • 2. Bratic, Ivana
    et al.
    Hench, Jürgen
    Södertörns högskola, Institutionen för livsvetenskaper.
    Henriksson, Johan
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Antebi, Adam
    Bürglin, Thomas R.
    Trifunovic, Aleksandra
    Mitochondrial DNA level, but not active replicase, is essential for Caenorhabditis elegans development2009Inngår i: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 37, nr 6, s. 1817-1828Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A number of studies showed that the development and the lifespan of Caenorhabditis elegans is dependent on mitochondrial function. In this study, we addressed the role of mitochondrial DNA levels and mtDNA maintenance in development of C. elegans by analyzing deletion mutants for mitochondrial polymerase gamma (polg-1(ok1548)). Surprisingly, even though previous studies in other model organisms showed necessity of polymerase gamma for embryonic development, homozygous polg-1(ok1548) mutants had normal development and reached adulthood without any morphological defects. However, polg-1 deficient animals have a seriously compromised gonadal function as a result of severe mitochondrial depletion, leading to sterility and shortened lifespan. Our results indicate that the gonad is the primary site of mtDNA replication, whilst the mtDNA of adult somatic tissues mainly stems from the developing embryo. Furthermore, we show that the mtDNA copy number shows great plasticity as it can be almost tripled as a response to the environmental stimuli. Finally, we show that the mtDNA copy number is an essential limiting factor for the worm development and therefore, a number of mechanisms set to maintain mtDNA levels exist, ensuring a normal development of C. elegans even in the absence of the mitochondrial replicase.

  • 3.
    Burglin, Thomas R
    Södertörns högskola, Avdelning Naturvetenskap.
    The homeobox genes of Encephalitozoon cuniculi (Microsporidia) reveal a putative mating-type locus2003Inngår i: Development, Genes and Evolution, ISSN 0949-944X, E-ISSN 1432-041X, Vol. 213, nr 1, s. 50-52Artikkel i tidsskrift (Fagfellevurdert)
  • 4.
    Bürglin, Thomas R.
    Södertörns högskola, Institutionen för livsvetenskaper.
    Evolution of hedgehog and hedgehog-related genes, their origin from Hog proteins in ancestral eukaryotes and discovery of a novel Hint motif2008Inngår i: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 9, s. 127-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: The Hedgehog (Hh) signaling pathway plays important roles in human and animal development as well as in carcinogenesis. Hh molecules have been found in both protostomes and deuterostomes, but curiously the nematode Caenorhabditis elegans lacks a bona-fide Hh. Instead a series of Hh-related proteins are found, which share the Hint/Hog domain with Hh, but have distinct N-termini. Results: We performed extensive genome searches such as the cnidarian Nematostella vectensis and several nematodes to gain further insights into Hh evolution. We found six genes in N. vectensis with a relationship to Hh: two Hh genes, one gene with a Hh N-terminal domain fused to a Willebrand factor type A domain (VWA), and three genes containing Hint/Hog domains with distinct novel N-termini. In the nematode Brugia malayi we find the same types of hh-related genes as in C. elegans. In the more distantly related Enoplea nematodes Xiphinema and Trichinella spiralis we find a bona-fide Hh. In addition, T. spiralis also has a quahog gene like C. elegans, and there are several additional hh-related genes, some of which have secreted N-terminal domains of only 15 to 25 residues. Examination of other Hh pathway components revealed that T. spiralis - like C. elegans - lacks some of these components. Extending our search to all eukaryotes, we recovered genes containing a Hog domain similar to Hh from many different groups of protists. In addition, we identified a novel Hint gene family present in many eukaryote groups that encodes a VWA domain fused to a distinct Hint domain we call Vint. Further members of a poorly characterized Hint family were also retrieved from bacteria. Conclusion: In Cnidaria and nematodes the evolution of hh genes occurred in parallel to the evolution of other genes that contain a Hog domain but have different N-termini. The fact that Hog genes comprising a secreted N-terminus and a Hog domain are found in many protists indicates that this gene family must have arisen in very early eukaryotic evolution, and gave rise eventually to hh and hh-related genes in animals. The results indicate a hitherto unsuspected ability of Hog domain encoding genes to evolve new N-termini. In one instance in Cnidaria, the Hh N-terminal signaling domain is associated with a VWA domain and lacks a Hog domain, suggesting a modular mode of evolution also for the N-terminal domain. The Hog domain proteins, the inteins and VWA-Vint proteins are three families of Hint domain proteins that evolved in parallel in eukaryotes.

  • 5.
    Bürglin, Thomas R.
    Södertörns högskola, Institutionen för livsvetenskaper.
    The Hedgehog protein family2008Inngår i: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 9, nr 11, s. 241-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Hedgehog (Hh) pathway is one of the fundamental signal transduction pathways in animal development and is also involved in stem-cell maintenance and carcinogenesis. The hedgehog (hh) gene was first discovered in Drosophila, and members of the family have since been found in most metazoa. Hh proteins are composed of two domains, an amino-terminal domain HhN, which has the biological signal activity, and a carboxy-terminal autocatalytic domain HhC, which cleaves Hh into two parts in an intramolecular reaction and adds a cholesterol moiety to HhN. HhC has sequence similarity to the self-splicing inteins, and the shared region is termed Hint. New classes of proteins containing the Hint domain have been discovered recently in bacteria and eukaryotes, and the Hog class, of which Hh proteins comprise one family, is widespread throughout eukaryotes. The non-Hh Hog proteins have carboxy-terminal domains ( the Hog domain) highly similar to HhC, although they lack the HhN domain, and instead have other amino-terminal domains. Hog proteins are found in many protists, but the Hh family emerged only in early metazoan evolution. HhN is modified by cholesterol at its carboxyl terminus and by palmitate at its amino terminus in both flies and mammals. The modified HhN is released from the cell and travels through the extracellular space. On binding its receptor Patched, it relieves the inhibition that Patched exerts on Smoothened, a G-protein-coupled receptor. The resulting signaling cascade converges on the transcription factor Cubitus interruptus (Ci), or its mammalian counterparts, the Gli proteins, which activate or repress target genes.

  • 6.
    Bürglin, Thomas R.
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    Kuwabara, P. E.
    Homologs of the Hh signalling network in C. elegans2006Inngår i: WormBook : the online review of C. elegans biology, ISSN 1551-8507, s. 1-14Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In Drosophila and vertebrates, Hedgehog (Hh) signalling is mediated by a cascade of genes, which play essential roles in cell proliferation and survival, and in patterning of the embryo, limb buds and organs. In C. elegans, this pathway has undergone considerable evolutionary divergence; genes encoding homologues of key pathway members, including Hh, Smoothened, Cos2, Fused and Suppressor of Fused, are absent. Surprisingly, over sixty proteins (i.e. WRT, GRD, GRL, and QUA), encoded by a set of genes collectively referred to as the Hh-related genes, and two co-orthologs (PTC-1,-3) of fly Patched, a Hh receptor, are present in C. elegans. Several of the Hh-related proteins are bipartite and all can potentially generate peptides with signalling activity, although none of these peptides shares obvious sequence similarity with Hh. In addition, the ptc-related (ptr) genes, which are present in a single copy in Drosophila and vertebrates and encode proteins closely related to Patched, have undergone an expansion in number in nematodes. A number of functions, including roles in molting, have been attributed to the C. elegans Hh-related, PTC and PTR proteins; most of these functions involve processes that are associated with the trafficking of proteins, sterols or sterol-modified proteins. Genes encoding other components of the Hh signalling pathway are also found in C. elegans, but their functions remain to be elucidated.

  • 7. Hao, Limin
    et al.
    Aspöck, Gudrun
    Bürglin, Thomas R
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    The hedgehog-related gene wrt-5 is essential for hypodermal development in Caenorhabditis elegans2006Inngår i: Developmental Biology, ISSN 0012-1606, E-ISSN 1095-564X, Vol. 290, nr 2, s. 323-336Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Caenorhabditis elegans genome encodes a series of hedgehog-related genes, which are thought to have evolved and diverged from an ancestral Hh gene. They are classified into several families based on their N-terminal domains. Here, we analyze the expression and function of a member of the warthog gene family, wrt-5, that lacks the Hint/Hog domain. wrt-5 is expressed in seam cells, the pharynx, pharyngeal-intestinal valve cells, neurons, neuronal support cells, the excretory cell, and the reproductive system. WRT-5 protein is secreted into the extracelluar space during embryogenesis. Furthermore, during larval development, WRT-5 protein is secreted into the pharyngeal lumen and the pharyngeal expression changes in a cyclical manner in phase with the molting cycle. Deletion mutations in wrt-5 cause embryonic lethality, which are temperature sensitive and more severe at 15 degrees C than at 25 degrees C. Animals that hatch exhibit variable abnormal morphology, for example, bagging worms, blistering, molting defects, or Roller phenotypes. We examined hypodermal cell junctions using the AJM-1: :GFP marker in the wrt-5 mutant background and observed cell boundary abnormalities in the arrested embryos. AJM-1: :GFP protein is also misplaced in pharyngeal muscle cells in the absence of WRT-5. In conclusion, we show that wrt-5 is an essential gene that - despite its lack of a Hint domain - has multiple functions in C. elegans and is implicated in cell shape integrity.

  • 8. Hao, Limin
    et al.
    Johnsen, Robert
    Lauter, Gilbert
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    Baillie, David
    Bürglin, Thomas R.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    Comprehensive analysis of gene expression patterns of hedgehog-related genes2006Inngår i: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 7, s. 280-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: The Caenorhabditis elegans genome encodes ten proteins that share sequence similarity with the Hedgehog signaling molecule through their C-terminal autoprocessing Hint/Hog domain. These proteins contain novel N-terminal domains, and C. elegans encodes dozens of additional proteins containing only these N-terminal domains. These gene families are called warthog, groundhog, ground-like and quahog, collectively called hedgehog (hh)-related genes. Previously, the expression pattern of seventeen genes was examined, which showed that they are primarily expressed in the ectoderm. Results: With the completion of the C. elegans genome sequence in November 2002, we reexamined and identified 61 hh-related ORFs. Further, we identified 49 hh-related ORFs in C. briggsae. ORF analysis revealed that 30% of the genes still had errors in their predictions and we improved these predictions here. We performed a comprehensive expression analysis using GFP fusions of the putative intergenic regulatory sequence with one or two transgenic lines for most genes. The hh-related genes are expressed in one or a few of the following tissues: hypodermis, seam cells, excretory duct and pore cells, vulval epithelial cells, rectal epithelial cells, pharyngeal muscle or marginal cells, arcade cells, support cells of sensory organs, and neuronal cells. Using time-lapse recordings, we discovered that some hh-related genes are expressed in a cyclical fashion in phase with molting during larval development. We also generated several translational GFP fusions, but they did not show any subcellular localization. In addition, we also studied the expression patterns of two genes with similarity to Drosophila frizzled, T23D8.1 and F27E11.3A, and the ortholog of the Drosophila gene dally-like, gpn-1, which is a heparan sulfate proteoglycan. The two frizzled homologs are expressed in a few neurons in the head, and gpn-1 is expressed in the pharynx. Finally, we compare the efficacy of our GFP expression effort with EST, OST and SAGE data. Conclusion: No bona-fide Hh signaling pathway is present in C. elegans. Given that the hh-related gene products have a predicted signal peptide for secretion, it is possible that they constitute components of the extracellular matrix (ECM). They might be associated with the cuticle or be present in soluble form in the body cavity. They might interact with the Patched or the Patched-related proteins in a manner similar to the interaction of Hedgehog with its receptor Patched.

  • 9. Hao, Limin
    et al.
    Mukherjee, Krishanu
    Liegeois, Samuel
    Baillie, David
    Labouesse, Michel
    Bürglin, Thomas R.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska institutet.
    The hedgehog-related gene qua-1 is required for molting in Caenorhabditis elegans2006Inngår i: Developmental Dynamics, ISSN 1058-8388, E-ISSN 1097-0177, Vol. 235, nr 6, s. 1469-1481Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Caenorhabditis elegans genome encodes ten proteins that share similarity with Hedgehog through the C-terminal Hint/Hog domain. While most genes are members of larger gene families, qua-1 is a single copy gene. Here we show that orthologs of qua-1 exist in many nematodes, including Brugia malayi, which shared a common ancestor with C. elegans about 300 million years ago. The QUA-1 proteins contain an N-terminal domain, the Qua domain, that is highly conserved, but whose molecular function is not known. We have studied the expression pattern of qua-1 in C. elegans using a qua-1::GFP transcriptional fusion. qua-1 is mainly expressed in hyp1 to hyp11 hypodermal cells, but not in seam cells. It is also expressed in intestinal and rectal cells, sensilla support cells, and the P cell lineage in L1. The expression of qua-1::GFP undergoes cyclical changes during development in phase with the molting cycle. It accumulates prior to molting and disappears between molts. Disruption of the qua-1 gene function through an internal deletion that causes a frame shift with premature stop in the middle of the gene results in strong lethality. The animals arrest in the early larval stages due to defects in molting. Electron microscopy reveals double cuticles due to defective ecdysis, but no obvious defects are seen in the hypodermis. Qua domain-only::GFP and full-length QUA-1::GFP fusion constructs are secreted and associated with the overlying cuticle, but only QUA-1::GFP rescues the mutant phenotype. Our results suggest that both the Hint/Hog domain and Qua domain are critically required for the function of QUA-1.

  • 10.
    Hench, Jürgen
    et al.
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik. Karolinska Institutet.
    Henriksson, Johan
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik. Karolinska Instiututet.
    Abou-Zied, Akram M
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik. Karolinska Institutet.
    Lüppert, Martin
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik. Karolinska Instiutetet.
    Dethlefsen, Johan
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik. Karolinska Institutet.
    Mukherjee, Krishanu
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik. Karolinska Intitutet.
    Tong, Yong Guang
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik. Karolinska Intitutet.
    Tang, Lois
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik. Karolinska Institutet.
    Gangishetti, Umesh
    Karolinska Institutet.
    Baillie, David L
    Simon Fraser University, Burnaby, British Columbia, Canada.
    Bürglin, Thomas R
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik. Karolinska Institutet.
    The Homeobox Genes of Caenorhabditis elegans and Insights into Their Spatio-Temporal Expression Dynamics during Embryogenesis2015Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, nr 5, artikkel-id e0126947Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Homeobox genes play crucial roles for the development of multicellular eukaryotes. We have generated a revised list of all homeobox genes for Caenorhabditis elegans and provide a nomenclature for the previously unnamed ones. We show that, out of 103 homeobox genes, 70 are co-orthologous to human homeobox genes. 14 are highly divergent, lacking an obvious ortholog even in other Caenorhabditis species. One of these homeobox genes encodes 12 homeodomains, while three other highly divergent homeobox genes encode a novel type of double homeodomain, termed HOCHOB. To understand how transcription factors regulate cell fate during development, precise spatio-temporal expression data need to be obtained. Using a new imaging framework that we developed, Endrov, we have generated spatio-temporal expression profiles during embryogenesis of over 60 homeobox genes, as well as a number of other developmental control genes using GFP reporters. We used dynamic feedback during recording to automatically adjust the camera exposure time in order to increase the dynamic range beyond the limitations of the camera. We have applied the new framework to examine homeobox gene expression patterns and provide an analysis of these patterns. The methods we developed to analyze and quantify expression data are not only suitable for C. elegans, but can be applied to other model systems or even to tissue culture systems.

  • 11.
    Hench, Jürgen
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper.
    Henriksson, Johan
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Lüppert, Martin
    Södertörns högskola, Institutionen för livsvetenskaper.
    Bürglin, Thomas R.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Spatio-temporal reference model of Caenorhabditis elegans embryogenesis with cell contact maps2009Inngår i: Developmental Biology, ISSN 0012-1606, E-ISSN 1095-564X, Vol. 333, nr 1, s. 1-13Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The nematode Caenorhabditis elegans has been used as a model for developmental biology for decades. Still, the few publicly available spatio-temporal (4D) data sets have conflicting information regarding variability of cell positions and are not well-suited for a standard 4D embryonic model, due to compression. We have recorded six uncompressed embryos, and determined their lineage and 4D coordinates, including nuclear radii, until the end of gastrulation. We find a remarkable degree of stability in the cell positions, as well as little rotational movement, which allowed us to combine the data into a single reference model of C. elegans embryogenesis. Using Voronoi decomposition we generated the list of all predicted cell contacts during early embryogenesis and calculated these contacts up to the similar to 150 cell stage, and find that about 1500 contacts last 2.5 min or longer. The cell contact map allows for comparison of multiple 4D data sets, e. g., mutants or related species, at the cellular level. A comparison of our uncompressed 4D model with a compressed embryo shows that up to 40% of the cell contacts can be different. To visualize the 4D model interactively we developed a software utility. Our model provides an anatomical resource and can serve as foundation to display 4D expression data, a basis for developmental systems biology.

  • 12.
    Henriksson, Johan
    et al.
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik. Karolinska Institute.
    Hench, Jürgen
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik. Karolinska Institute.
    Tong, Yong Guang
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik. Karolinska Institute.
    Johansson, Arvid
    Johansson, David
    Bürglin, Thomas R.
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik. Karolinska Institute.
    Endrov: an integrated platform for image analysis2013Inngår i: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 10, nr 6, s. 454-456Artikkel i tidsskrift (Fagfellevurdert)
  • 13.
    Kagoshima, Hiroshi
    et al.
    Universität Basel, Basel, Switzerland /National Institute of Genetics, Shizuoka, Japan / Research Organization of Information and Systems (ROIS), Tokyo, Japan.
    Cassata, Giuseppe
    Universität Basel, Basel, Switzerland.
    Tong, Yong Guang
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Biologi. Karolinska Institute.
    Pujol, Nathalie
    Aix-Marseille Université, Marseille, France.
    Niklaus, Gisela
    Universität Basel, Basel, Switzerland.
    Bürglin, Thomas R.
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Biologi. Karolinska Institute / Universität Basel, Basel, Switzerland.
    The LIM homeobox gene ceh-14 is required for phasmid function and neurite outgrowth2013Inngår i: Developmental Biology, ISSN 0012-1606, E-ISSN 1095-564X, Vol. 380, nr 2, s. 314-323Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Transcription factors play key roles in cell fate specification and cell differentiation. Previously, we showed that the LIM homeodomain factor CEH-14 is expressed in the AFD neurons where it is required for thermotaxis behavior in Caenorhabditis elegans. Here, we show that ceh-14 is expressed in the phasmid sensory neurons, PHA and PHB, a number of neurons in the tail, i.e., PHC, DVC, PVC, PVN, PVQ PVT, PVW and PVR, as well as the touch neurons. Analysis of the promoter region shows that important regulatory elements for the expression in most neurons reside from -4 kb to -1.65 kb upstream of the start codon. Further, within the first introns are elements for expression in the hypodermis. Phylogenetic footprinting revealed numerous conserved motifs in these regions. In addition to the existing deletion mutation ceh-14(ch3), we isolated a new allele, ceh-14(ch2), in which only one LIM domain is disrupted. The latter mutant allele is partially defective for thermosensation. Analysis of both mutant alleles showed that they are defective in phasmid dye-filling. However, the cell body, dendritic outgrowth and ciliated endings of PHA and PHB appear normal, indicating that ceh-14 is not required for growth. The loss of a LIM domain in the ceh-14(ch2) allele causes a partial loss-of-function phenotype. Examination of the neurites of ALA and tail neurons using a ceh-14::GFP reporter shows abnormal axonal outgrowth and pathfinding.

  • 14. Mukherjee, K.
    et al.
    Brocchieri, L.
    Bürglin, Tomas R.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska institutet.
    A comprehensive classification and evolutionary analysis of plant homeobox genes2009Inngår i: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 26, nr 12, s. 2775-2794Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The full complement of homeobox transcription factor sequences, including genes and pseudogenes, was determined from the analysis of 10 complete genomes from flowering plants, moss, Selaginella, unicellular green algae, and red algae. Our exhaustive genome-wide searches resulted in the discovery in each class of a greater number of homeobox genes than previously reported. All homeobox genes can be unambiguously classified by sequence evolutionary analysis into 14 distinct classes also characterized by conserved intron-exon structure and by unique codomain architectures. We identified many new genes belonging to previously defined classes (HD-ZIP I to IV, BEL, KNOX, PLINC, WOX). Other newly identified genes allowed us to characterize PHD, DDT, NDX, and LD genes as members of four new evolutionary classes and to define two additional classes, which we named SAWADEE and PINTOX. Our comprehensive analysis allowed us to identify several newly characterized conserved motifs, including novel zinc finger motifs in SAWADEE and DDT. Members of the BEL and KNOX classes were found in Chlorobionta (green plants) and in Rhodophyta. We found representatives of the DDT, WOX, and PINTOX classes only in green plants, including unicellular green algae, moss, and vascular plants. All 14 homeobox gene classes were represented in flowering plants, Selaginella, and moss, suggesting that they had already differentiated in the last common ancestor of moss and vascular plants.

  • 15.
    Mukherjee, Krishanu
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    Bürglin, Thomas R.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    Comprehensive analysis of animal TALE homeobox genes: New conserved motifs and cases of accelerated evolution2007Inngår i: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 65, nr 2, s. 137-153Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    TALE homeodomain proteins are an ancient subgroup within the group of homeodomain transcription factors that play important roles in animal, plant, and fungal development. We have extracted the full complement of TALE superclass homeobox genes from the genome projects of seven protostomes, seven deuterostomes, and Nematostella. This was supplemented with TALE homeobox genes from additional species and phylogenetic analyses were carried out with 276 sequences. We found 20 homeobox genes and 4 pseudogenes in humans, 21 genes in mouse, 8 genes in Drosophila, and 5 genes plus one truncated gene in Caenorhabditis elegans. Apart from the previously identified TALE classes MEIS, PBC, IRO, and TGIF, a novel class is identified, termed MOHAWK (MKX). Further, we show that the MEIS class can be divided into two families, PREP and MEIS. Prep genes have previously only been described in vertebrates but are lacking in Drosophila. Here we identify orthologues in other insect taxa as well as in the cnidarian Nematostella. In C. elegans, a divergent Prep protein has lost the homeodomain. Full-length multiple sequence alignment of the protostome and deuterostome sequences allowed us to identify several novel conserved motifs within the MKX, TGIF, and MEIS classes. Phylogenetic analyses revealed fast-evolving PBC class genes; in particular, some X-linked PBC genes in nematodes are subject to rapid evolution. In addition, several instances of gene loss were identified. In conclusion, our comprehensive analysis provides a defining framework for the classification of animal TALE homeobox genes and the understanding of their evolution.

  • 16.
    Mukherjee, Krishanu
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper.
    Bürglin, Thomas R
    Södertörns högskola, Institutionen för livsvetenskaper.
    MEKHLA, a novel domain with similarity to PAS domains, is fused to plant homeodomain-leucine zipper III proteins2006Inngår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 140, nr 4, s. 1142-1150Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Homeodomain (HD) proteins play important roles in the development of plants, fungi, and animals. Here we identify a novel domain, MEKHLA, in the C terminus of HD-Leu zipper (HD-ZIP) III plant HD proteins that shares similarity with a group of bacterial proteins and a protein from the green alga Chlamydomonas reinhardtii. The group of bacterial MEKHLA proteins is found in cyanobacteria and other bacteria often found associated with plants. Phylogenetic analysis suggests that a MEKHLA protein transferred, possibly from a cyanobacterium or an early chloroplast, into the nuclear genome of an early plant in a first step, and attached itself to the C terminus of an HD-ZIP IV homeobox gene in a second step. Further position-specific iterated-BLAST searches with the bacterial MEKHLA proteins revealed a subregion within the MEKHLA domain that shares significant similarity with the PAS domain. The PAS domain is a sensory module found in many proteins through all kingdoms of life. It is involved in light, oxygen, and redox potential sensation. The fact that HD-ZIP III proteins are transcription factors that have this sensory domain attached to their C terminus uncovers a potential new signaling pathway in plants.

  • 17.
    Pérez-Bercoff, Åsa
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute / Chalmers Universtiy.
    Koch, Johan
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    Bürglin, Thomas R.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    LogoBar: Bar graph visualization of protein logos with gaps2006Inngår i: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 22, nr 1, s. 112-114Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Summary: LogoBar is a Java application to display protein sequence logos. In our software gaps are accounted for when calculating the information content present at each residue position in a multiple alignment. The resulting logo is displayed as a graph consisting of bars, although traditional letter representation is also possible. Amino acids are displayed from the bottom up with decreasing frequencies i.e. the most abundant residue is placed at the bottom of the logo. The bars can be color-coded according to user specifications. Gaps in the alignment are also displayed, either on top or at the bottom of the logo. Furthermore, residues can either be arranged according to their relative abundance or grouped according to user criteria to emphasize the conserved nature of particular positions.

  • 18.
    Sagemark, Johan
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    Elgan, Tobias H.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    Bürglin, Thomas R.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    Johansson, Catrine
    Holmgren, Arne
    Berndt, Kurt D.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    Redox properties and evolution of human glutaredoxins2007Inngår i: Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 68, nr 4, s. 879-892Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Glutaredoxins (Grxs) are glutathione-dependent oxidoreductases that belong to the thioredoxin superfamily catalyzing thiol-disulfide exchange reactions via active site cysteine residues. Focusing on the human dithiol glutaredoxins having a C-X-Y-C active site sequence motif, the redox potentials of hGrxl and hGrx2 were determined to be -232 and -221 mV, respectively, using a combination of redox buffers, protein-protein equilibrium and thermodynamic linkage. In addition, a nonactive site disulfide was identified between Cys28 and Cys.113 in hGrx2 using redox buffers and chemical digestion. This disulfide confers nearly five kcal mol-1 additional stability by linking the C-terminal helix to the bulk of the protein. The redox potential of this nonactive site disulfide was determined to be -317 mVand is thus expected to be present in all but the most reducing conditions in vivo. As all human glutaredoxins contain additional nonactive site cysteine residues, a full phylogenetic analysis was performed to help elucidate their structural and functional roles. Three distinct groups were found: Grx1, Grx2, and Grx5, the latter representing a highly conserved group of monothiol glutaredoxins having a C-G-F-S active site sequence, with clear homologs from bacteria to human. Grx1 and Grx2 diverged from a common ancestor before the origin vertebrates, possibly even earlier in animal evolution. The highly stabilizing nonactive site disulfide observed in hGrx2 is found to be a conserved feature within the deuterostomes and appears to be the only additional conserved intramolecular disulfide within the glutaredoxins.

  • 19.
    Tong, Yong-Guang
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Bürglin, Thomas R.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Conditions for dye-filling of sensory neurons in Caenorhabditis elegans2010Inngår i: Journal of Neuroscience Methods, ISSN 0165-0270, E-ISSN 1872-678X, Vol. 188, nr 1, s. 58-61Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Dye-filling is a common method used to stain Caenorhabditis elegans ensory neurons in vivo. While the amphids and phasmids are easy to tain, a subset of sensory neurons, the IL2 neurons, are difficult to tain reproducibly. Here we examined the conditions under which the IL2 eurons take up the lipophilic fluorescent dye DiI. We find that IL2 ye-filling depends on salt concentration, but not osmolarity. Low salt rior and during incubation is important for efficient dye uptake. dditional parameters that affect dye-filling are the speed of shaking uring incubation and the addition of detergents. Our modified ye-filling procedure provides a reliable method to distinguish mutant lleles that stain amphids and phasmids, IL2 neurons, or both. An dditional benefit is that it can also stain the excretory duct. The ethod allows genetic screens to be performed to identify mutants that electively affect only one of the sensory structures or the excretory uct.

  • 20.
    Tong, Yong-Guang
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Meenon, K.
    Meenon, K.
    Prétôt, R.
    Viktorin-Aspöck, G.
    Bürglin, Thomas R.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    A regulatory network of homeobox genes is required for the function of the Caenorhabditis elegans excretory cellManuskript (preprint) (Annet vitenskapelig)
  • 21.
    Xue-Franzen, Yongtao
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska Institutet.
    Johnsson, Anna
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska Intitutet.
    Brodin, David
    Karolinska Institutet.
    Henriksson, Johan
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska Institutet.
    Bürglin, Thomas R.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska Institutet.
    Wright, Anthony P. H.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska Institutet.
    Genome-wide characterisation of the Gcn5 histone acetyltransferase in budding yeast during stress adaptation reveals evolutionarily conserved and diverged roles2010Inngår i: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 11, artikkel-id 200Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Gcn5 is a transcriptional coactivator with histone cetyltransferase activity that is conserved with regard to structure as ell as its histone substrates throughout the eukaryotes. Gene egulatory networks within cells are thought to be evolutionarily iverged. The use of evolutionarily divergent yeast species, such as S. erevisiae and S. pombe, which can be studied under similar nvironmental conditions, provides an opportunity to examine the nterface between conserved regulatory components and their cellular pplications in different organisms. esults: We show that Gcn5 is important for a common set of stress esponses in evolutionarily diverged yeast species and that the activity f the conserved histone acetyltransferase domain is required. We define group of KCl stress response genes in S. cerevisiae that are pecifically dependent on Gcn5. Gcn5 is localised to many Gcn5-dependent enes including Gcn5 repressed targets such as FLO8. Gcn5 regulates ivergent sets of KCl responsive genes in S. cerevisiae and S. pombe. enome-wide localization studies showed a tendency for redistribution of cn5 during KCl stress adaptation in S. cerevisiae from short genes to he transcribed regions of long genes. An analogous redistribution was ot observed in S. pombe. onclusions: Gcn5 is required for the regulation of divergent sets of Cl stress-response genes in S. cerevisiae and S. pombe even though it s required a common group of stress responses, including the response o KCl. Genes that are physically associated with Gcn5 require its ctivity for their repression or activation during stress adaptation, roviding support for a role of Gcn5 as a corepressor as well as a oactivator. The tendency of Gcn5 to re-localise to the transcribed egions of long genes during KCl stress adaptation suggests that Gcn5 lays a specific role in the expression of long genes under adaptive onditions, perhaps by regulating transcriptional elongation as has been een for Gcn5 in S. pombe. Interestingly an analogous redistribution of cn5 is not seen in S. pombe. The study thus provides important new nsights in relation to why coregulators like Gcn5 are required for the orrect expression of some genes but not others.

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