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  • 1.
    Hench, Jürgen
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies. Karolinska Institutet.
    Henriksson, Johan
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies. Karolinska Instiututet.
    Abou-Zied, Akram M
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies. Karolinska Institutet.
    Lüppert, Martin
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies. Karolinska Instiutetet.
    Dethlefsen, Johan
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies. Karolinska Institutet.
    Mukherjee, Krishanu
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies. Karolinska Intitutet.
    Tong, Yong Guang
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies. Karolinska Intitutet.
    Tang, Lois
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies. Karolinska Institutet.
    Gangishetti, Umesh
    Karolinska Institutet.
    Baillie, David L
    Simon Fraser University, Burnaby, British Columbia, Canada.
    Bürglin, Thomas R
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies. Karolinska Institutet.
    The Homeobox Genes of Caenorhabditis elegans and Insights into Their Spatio-Temporal Expression Dynamics during Embryogenesis2015In: PLOS ONE, E-ISSN 1932-6203, Vol. 10, no 5, article id e0126947Article in journal (Refereed)
    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.

  • 2.
    Mukherjee, Krishanu
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Bürglin, Thomas R.
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Comprehensive analysis of animal TALE homeobox genes: New conserved motifs and cases of accelerated evolution2007In: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 65, no 2, p. 137-153Article in journal (Refereed)
    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.

  • 3.
    Mukherjee, Krishanu
    et al.
    Södertörn University, School of Life Sciences.
    Bürglin, Thomas R
    Södertörn University, School of Life Sciences.
    MEKHLA, a novel domain with similarity to PAS domains, is fused to plant homeodomain-leucine zipper III proteins2006In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 140, no 4, p. 1142-1150Article in journal (Refereed)
    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.

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