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Regulatory function of homeobox genes in the development of Caenorhabditis elegans
Södertörn University, School of Life Sciences, Molecular biology. Karolinska Intsitutet.
2010 (English)Doctoral thesis, comprehensive summary (Other academic)Text
Abstract [en]

The nematode worm Caenorhabditis elegans has been widely used as a genetic model for over 40 years to investigate developmental control genes. In this thesis, I studied the roles of several homeobox genes and a novel RNA binding protein (RBD) in the development of C. elegans to understand the function of these genes in higher organisms. Homeobox genes are transcriptional regulators that are highly conserved in evolution and play important domains in eukaryotes, and genes encoding this domain play roles in a wide variety of post-transcriptional gene regulation processes. In paper I, we characterized a novel protein, RNA binding domain-1 (RBD-1), which is involved in ribosome biogenesis. This protein contains six consensus RNA-binding domains and is conserved as to sequence, domain organization, and subcellular localization from yeast to human. RBD-1 is essential for the development of C. elegans. The RNAi experiments using the cDNA of RBD-1 demonstrated various abnormalities in the C. elegans development, such as defects in morphology (dumpy), incomplete molting, and defective gonadal and vulval development. Animals depleted for RBD-1 arrested mainly at the L1 larval stage. In the course of studying the homeobox genes, we often used the dye-filling assay. It is the simplest method presently used to assay the structural integrity of sensory cilia. In paper II, we optimized conditions, in which reliable staining of the inner labial (IL2) neurons could be obtained, namely in low salt conditions, in the presence of determethod to distinguish mutant alleles that stain amphids and phasmids, and IL2 neurons. Using this assay, we found that a mutation in the POU homeobox gene unc-86 abolished dye-filling in IL2 neurons but not amphids and phasmids. mids. In Paper III, we showed that the LIM homeobox gene ceh-14 was expressed in other sensory neurons and interneurons, including the phasmid neurons and the ALA interneuron, while previously it was shown that ceh-14 is expressed in the AFD neurons and required for thermotaxis behavior in C. elegans. ceh-14 mutant animals displayed defects in dendrite outgrowth of the phasmid neurons, while the ALA interneuron and some tail neurons showed ceh-14 and the paired-like homeobox gene ceh-17 act in the separate pathway to control normal axonal outgrowth of ALA neuron. Overexpression of CEH-14 in the nervous system may titrate out interacting factors, such as LDB-1, which caused developmental defects In paper IV, we investigated the function of four homeobox genes, ceh-6, ceh-26, ttx-1 and ceh-37, in the excretory cell development. We showed that the POU-III class homeobox gene ceh-6, the Prospero class homeobox gene ceh-26, and two otd/Otx family homeobox genes, ceh-37 and ttx-1 formed a regulatory hierarchy required for the development and function of the excretory cell in C. elegans. The excretory cell is required for maintaining osmotic balance and excreting waste products. While ceh-6 has previously been demonstrated to play a role in the excretory cell patterning, we showed here that ceh-26 and ceh-37 are expressed in the excretory cell. ceh-26 mutants arrested in early larval development with defects characteristic for a lack of excretory cell function. Double mutant of the otd/Otx genes ceh-37 and ttx-1 was displaying larval arrest, consistent with the excretory cell dysfunction, which indicates that there is functional redundancy between these two genes. Using mutant alleles and RNAi, we showed that ceh-26::GFP and ceh-37::GFP was down-regulated in ceh-6 mutants. Further, we found that ceh-37::GFP was down-regulated in the ceh-26 genes, such as channel proteins (the target genes ) that are expressed in the excretory cell and found that only a subset of the genes regulated by ceh-6 was also regulated by ceh-37/ttx-1. We mapped the promoter regions of ceh-26 and of the target gene clh-4 to identify putative homeodomain proteins binding sites. Given that these homeobox genes are well conserved in evolution, we may expect that parts of this cascade are also conserved in other organisms.

Place, publisher, year, edition, pages
Stockholm: Karolinska Institutet , 2010. , 47 p.
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:sh:diva-29738ISBN: 978-91-7457-018-2OAI: oai:DiVA.org:sh-29738DiVA: diva2:911770
Available from: 2016-03-14 Created: 2016-03-14 Last updated: 2016-03-14Bibliographically approved
List of papers
1. A novel conserved RNA-binding domain protein, RBD-1, is essential for ribosome biogenesis
Open this publication in new window or tab >>A novel conserved RNA-binding domain protein, RBD-1, is essential for ribosome biogenesis
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2002 (English)In: Molecular Biology of the Cell, ISSN 1059-1524, E-ISSN 1939-4586, Vol. 13, no 10, 3683-3695 p.Article in journal (Refereed) Published
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.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:sh:diva-29737 (URN)10.1091/mbc.E02-03-0138 (DOI)12388766 (PubMedID)
Available from: 2016-03-14 Created: 2016-03-14 Last updated: 2016-03-14Bibliographically approved
2. Conditions for dye-filling of sensory neurons in Caenorhabditis elegans
Open this publication in new window or tab >>Conditions for dye-filling of sensory neurons in Caenorhabditis elegans
2010 (English)In: Journal of Neuroscience Methods, ISSN 0165-0270, E-ISSN 1872-678X, Vol. 188, no 1, 58-61 p.Article in journal (Refereed) Published
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.

National Category
Neurology
Identifiers
urn:nbn:se:sh:diva-13709 (URN)10.1016/j.jneumeth.2010.02.003 (DOI)000276866400009 ()20149821 (PubMedID)2-s2.0-77950460160 (ScopusID)
Available from: 2011-12-06 Created: 2011-12-06 Last updated: 2016-03-14Bibliographically approved
3. The LIM homeobox gene ceh-14 is required for phasmid function and neurite outgrowth
Open this publication in new window or tab >>The LIM homeobox gene ceh-14 is required for phasmid function and neurite outgrowth
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2013 (English)In: Developmental Biology, ISSN 0012-1606, E-ISSN 1095-564X, Vol. 380, no 2, 314-323 p.Article in journal (Refereed) Published
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.

National Category
Biological Sciences
Identifiers
urn:nbn:se:sh:diva-19637 (URN)10.1016/j.ydbio.2013.04.009 (DOI)000322297900015 ()23608457 (PubMedID)2-s2.0-84879881843 (ScopusID)
Note

Som manuskript i avhandling. As manuscript in dissertation.

Available from: 2013-09-02 Created: 2013-09-02 Last updated: 2016-03-14Bibliographically approved
4. A regulatory network of homeobox genes is required for the function of the Caenorhabditis elegans excretory cell
Open this publication in new window or tab >>A regulatory network of homeobox genes is required for the function of the Caenorhabditis elegans excretory cell
Show others...
(English)Manuscript (preprint) (Other academic)
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:sh:diva-29736 (URN)
Note

Som manuskript i avhandling. As manuscript in dissertation.

Available from: 2016-03-14 Created: 2016-03-14 Last updated: 2016-03-14Bibliographically approved

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