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  • 1. Agalou, Adamantia
    et al.
    Purwantomo, Sigit
    Övernäs, Elin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Johannesson, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Zhu, Xiaoyi
    Estiati, Amy
    de Kam, Rolf J.
    Engström, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Slamet-Loedin, Inez H.
    Zhu, Zhen
    Wang, Mei
    Xiong, Lizhong
    Meijer, Annemarie H.
    Ouwerkerk, Pieter B. F.
    A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members2008In: Plant Molecular Biology, ISSN 0167-4412, E-ISSN 1573-5028, Vol. 66, no 1-2, p. 87-103Article in journal (Refereed)
    Abstract [en]

    The homeodomain leucine zipper (HD-Zip) genes encode transcription factors that have diverse functions in plant development and have often been implicated in stress adaptation. The HD-Zip genes are the most abundant group of homeobox (HB) genes in plants and do not occur in other eukaryotes. This paper describes the complete annotation of the HD-Zip families I, II and III from rice and compares these gene families with Arabidopsis in a phylogeny reconstruction. Orthologous pairs of rice and Arabidopsis HD-Zip genes were predicted based on neighbour joining and maximum parsimony (MP) trees with support of conserved intron-exon organization. Additionally, a number of HD-Zip genes appeared to be unique to rice. Searching of EST and cDNA databases and expression analysis using RT-PCR showed that 30 out of 31 predicted rice HD-Zip genes are expressed. Most HD-Zip genes were broadly expressed in mature plants and seedlings, but others showed more organ specific patterns. Like in Arabidopsis and other dicots, a subset of the rice HD-Zip I and II genes was found to be regulated by drought stress. We identified both drought-induced and drought-repressed HD-Zip genes and demonstrate that these genes are differentially regulated in drought-sensitive versus drought-tolerant rice cultivars. The drought-repressed HD-Zip family I gene, Oshox4, was selected for promoter-GUS analysis, showing that drought-responsiveness of Oshox4 is controlled by the promoter and that Oshox4 expression is predominantly vascular-specific. Loss-of-function analysis of Oshox4 revealed no specific phenotype, but overexpression analysis suggested a role for Oshox4 in elongation and maturation processes.

  • 2.
    Carlsbecker, Annelie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Lee, Ji-Young
    Roberts, Christina J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Dettmer, Jan
    Lehesranta, Satu
    Zhou, Jing
    Lindgren, Ove
    Moreno-Risueno, Miguel A.
    Vatén, Anne
    Thitamadee, Siripong
    Campilho, Ana
    Sebastian, Jose
    Bowman, John L.
    Helariutta, Yka
    Benfey, Philip N.
    Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate2010In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 465, no 7296, p. 316-321Article in journal (Refereed)
    Abstract [en]

    A key question in developmental biology is how cells exchange positional information for proper patterning during organ development. In plant roots the radial tissue organization is highly conserved with a central vascular cylinder in which two water conducting cell types, protoxylem and metaxylem, are patterned centripetally. We show that this patterning occurs through crosstalk between the vascular cylinder and the surrounding endodermis mediated by cell-to-cell movement of a transcription factor in one direction and microRNAs in the other. SHORT ROOT, produced in the vascular cylinder, moves into the endodermis to activate SCARECROW. Together these transcription factors activate MIR165a and MIR166b. Endodermally produced microRNA165/6 then acts to degrade its target mRNAs encoding class III homeodomain-leucine zipper transcription factors in the endodermis and stele periphery. The resulting differential distribution of target mRNA in the vascular cylinder determines xylem cell types in a dosage-dependent manner.

  • 3.
    Costa, José Luis
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    The tRNALeu (UAA) Intron of Cyanobacteria: Towards Understanding a Genetic Marker2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The tRNALeu (UAA) intron has been recorded in the plastid genome of many algae and land plants and was the first intron to be discovered in cyanobacteria. In all known cases it interrupts the tRNALeu anticodon loop at a conserved position (U-intron-AA). Cyanobacteria are a diverse group of photosynthetic prokaryotes, some involved in symbiotic associations with a wide range of organisms. The most studied associations are those with plants, where strains of Nostoc are the common cyanobacterial partner. In this thesis two aspects of the biology of the cyanobacterial tRNALeu (UAA) intron are focused: first, the use of the intron as a genetic marker for studying the diversity and specificity of two cyanobacterial symbiosis (bryophytes and cycads) and second, the evolutionary patterns of the intron by using the unique data set generated from the diversity analysis.

    From the studies, many different Nostoc strains are involved in the two symbiotic associations, although no variation was observed within a single bryophyte cavity or cycad coralloid root. Furthermore, a certain level of temporal stability in the cyanobiont composition of the bryophyte population was found and, in the cycad association different coralloid roots from a single specimen may harbor different cyanobacteria. That a minor cyanobiont could have avoided detection is still possible but unlikely. The sequence alignment of the Nostoc tRNALeu (UAA) introns reveals great sequence similarity with size variation only found in the structural element P6b. This element was found to consist of heptanucleotide repeats and of other non-repetitive genetic elements (NIS elements). The sporadic occurrence of the NIS elements indicates recent origins and a mechanism for its dispersal is proposed.

    In this thesis new insights are given concerning cyanobacterial symbioses and also on the mechanisms involved in the evolution of an old genetic element: the tRNALeu (UAA) intron in cyanobacteria.

    List of papers
    1. Cyanobiont diversity within coralloid roots of selected cycad species
    Open this publication in new window or tab >>Cyanobiont diversity within coralloid roots of selected cycad species
    1999 (English)In: FEMS Microbiology Ecology, ISSN 0168-6496, Vol. 28, p. 85-91Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92108 (URN)
    Available from: 2004-09-23 Created: 2004-09-23 Last updated: 2012-08-22
    2. Sequenced based data supports a single Nostoc strain in coralloid roots of cycads
    Open this publication in new window or tab >>Sequenced based data supports a single Nostoc strain in coralloid roots of cycads
    2004 (English)In: FEMS Microbiology Ecology, ISSN 0168-6496, Vol. 49, p. 481-487Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92109 (URN)
    Available from: 2004-09-23 Created: 2004-09-23 Last updated: 2012-08-22
    3. Genetic diversity of Nostoc symbionts endophytically associated with two bryophyte species
    Open this publication in new window or tab >>Genetic diversity of Nostoc symbionts endophytically associated with two bryophyte species
    2001 (English)In: Applied and Environmental Microbiology, ISSN 0099-2240, Vol. 67, p. 4393-4396Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92110 (URN)
    Available from: 2004-09-23 Created: 2004-09-23 Last updated: 2012-08-22
    4. The cyanobacterial tRNA(Leu) (UAA) intron: Evolutionary patterns in a genetic marker
    Open this publication in new window or tab >>The cyanobacterial tRNA(Leu) (UAA) intron: Evolutionary patterns in a genetic marker
    2002 (English)In: Molecular Biology and Evolution, ISSN 0737-4038, Vol. 19, p. 850-857Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92111 (URN)
    Available from: 2004-09-23 Created: 2004-09-23 Last updated: 2012-08-22
    5. Dispersal of iterated sequences in the genome of the cyanobacterium Nostoc punctiforme
    Open this publication in new window or tab >>Dispersal of iterated sequences in the genome of the cyanobacterium Nostoc punctiforme
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-92112 (URN)
    Available from: 2004-09-23 Created: 2004-09-23 Last updated: 2010-01-14Bibliographically approved
  • 4.
    Costa, José Luis
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Elhai, Jeff
    Cousins, Sarah
    Lindblad, Peter
    Dispersal of iterated sequences in the genome of the cyanobacterium Nostoc punctiformeManuscript (Other (popular science, discussion, etc.))
  • 5.
    Costa, José Luis
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Martínez-Romero, Esperanza
    Lindblad, Peter
    Sequenced based data supports a single Nostoc strain in coralloid roots of cycads2004In: FEMS Microbiology Ecology, ISSN 0168-6496, Vol. 49, p. 481-487Article in journal (Refereed)
  • 6.
    Costa, José Luis
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Paulsrud, Per
    Lindblad, Peter
    Cyanobiont diversity within coralloid roots of selected cycad species1999In: FEMS Microbiology Ecology, ISSN 0168-6496, Vol. 28, p. 85-91Article in journal (Refereed)
  • 7.
    Costa, José Luis
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Paulsrud, Per
    Lindblad, Peter
    The cyanobacterial tRNA(Leu) (UAA) intron: Evolutionary patterns in a genetic marker2002In: Molecular Biology and Evolution, ISSN 0737-4038, Vol. 19, p. 850-857Article in journal (Refereed)
  • 8.
    Costa, José Luis
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Paulsrud, Per
    Rikkinen, Jouko
    Lindblad, Peter
    Genetic diversity of Nostoc symbionts endophytically associated with two bryophyte species2001In: Applied and Environmental Microbiology, ISSN 0099-2240, Vol. 67, p. 4393-4396Article in journal (Refereed)
  • 9.
    Costa, José-Luis
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Fysiologisk botanik. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Martínez Romero, Esperanza
    Lindblad, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Fysiologisk botanik. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Sequence based data supports a single Nostoc strain in individual coralloid roots of cycads2004In: FEMS Microbiology: Ecology, Vol. 49, p. 481-487Article in journal (Refereed)
    Abstract [en]

    The genertic diversity of cyanobacteria associated with cycads was examined using the tRNA Leu (UAA) intron as a genetic marker. Coralloid roots of both natural populations of the cycad Macrozamia riedlei (Fischer ex Gaudichaud-Beaupré) C.A. Gardner growing in Perth, Australia and cycads growing in greenhouses, also in Perth, were used and their respective cyanobionts analyzed. Several Nostoc strains were found to be involved in this symbiosis, both in natural populations and greenhouse-orginated cycads. However, only one strain was present in individual coralloid roots and in individual plants, even when analyzing different coralloid roots from the same plant. Moreover, when examining plants growing close to each other (female plants and their respective offspring) the same cyanobacterium was consistently present in the different coralloid roots. Whether this reflects a selective mechanism or merely the availability of Nostoc strains remains to be ascertained. The high cyanobacterial diversity in coralloid roots of cycads revealed by PCR fingerprinting is, therefore, contested. In this study, the potential probems of using different methods (e.g. PCR fingerprinting) to study the genetic diversity of symbiotic cyanobacteria, is also addressed.

  • 10.
    Eriksson, Tage
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Fridborg, Gunnar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Fysiologisk botanik vid Uppsala universitet: En historik2008Book (Other academic)
  • 11.
    Henriksson, Eva
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    The HDZip Class I Transcription Factors in Arabidopsis thaliana: Characterisation of HDZip Genes Involved in the Mediation of Environmental Signals2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Homeodomain leucine zipper (HDZip) proteins constitute a large family of transcription factors characterised by the presence of a DNA-binding homeodomain and an adjacent leucine zipper motif, which mediates protein-dimer formation. The HDZip genes of Arabidopsis have been divided into four classes, HDZip I-IV. This thesis describes the characterisation and phylogeny of the class I HDZip genes and focuses on the expression and function of four HDZip I genes, ATHB5, -6, -7 and -16.

    The phylogenetic analyses of the 17 HDZip I sequences defined six subclasses, supported by the intron patterning and the traced duplication history of the genes. The members within each subclass showed diversification in expression, suggesting that the cis regulatory regions of the closely related genes have undergone evolutionary changes. However, similarities in the gene expression patterns between genes also exist and external factors like the availability of water and quality of light directs the expression of a subset of HDZip I genes. Expression analyses revealed that the plant hormone abscisic acid (ABA) is involved as a systemic signal for the salt or osmoticum induced ATHB7 expression, whereas light signals mediated through the blue light photoreceptors was found to direct the expression of ATHB6.

    Phenotypic analyses of plants with altered levels of ATHB6 or ATHB16 suggested that these paralogous genes encode proteins with very similar functions. ATHB16 was shown to act as a negative regulator of leaf cell expansion, as a suppressor of the flowering time sensitivity to photoperiod and as a positive regulator of blue light dependent inhibition of hypocotyl growth. A similar role for ATHB6 in the regulation of hypocotyl elongation was recorded. Further, analyses of multiple loss-of-function plants demonstrated that ATHB5, -6 and -16 function at least in part redundantly in mediating light effects on hypocotyl elongation.

    List of papers
    1. HDZip class I genes in Arabidopsis: expression profiles and phylogenetic relationships
    Open this publication in new window or tab >>HDZip class I genes in Arabidopsis: expression profiles and phylogenetic relationships
    Show others...
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-92027 (URN)
    Available from: 2004-09-02 Created: 2004-09-02 Last updated: 2010-01-14Bibliographically approved
    2. Salt stress signalling and the role of calcium in the regulation of the Arabidopsis ATHB7 gene
    Open this publication in new window or tab >>Salt stress signalling and the role of calcium in the regulation of the Arabidopsis ATHB7 gene
    2005 (English)In: Plant, Cell and Environment, ISSN 0140-7791, E-ISSN 1365-3040, Vol. 28, no 2, p. 202-210Article in journal (Refereed) Published
    Abstract [en]

    In plants changes in cytosolic calcium ion concentrations ([Ca2+]cyt) have been detected after various stress treatments, including salt treatment. The involvement of a Ca2+ signal as an essential component of signalling pathways leading to downstream responses, such as gene expression, is supported only by a few studies. In this study the possible involvement of the salt stress-induced increase in [Ca2+]cyt in the signalling pathway leading to the induction of ATHB7, a homeobox gene encoding a homeodomain leucine zipper (HDZip) transcription factor was analysed. The salt-induced expression of ATHB7 was found to be independent of the Ca2+ signal evoked by salt. Instead, it was found that ATHB7 expression in shoots was not dependent on a direct contact with salt or osmoticum, whereas in roots, ATHB7 seemed to be induced by the direct contact, indicating that signals from roots cause systemic induction of ATHB7. Abscisic acid (ABA) or ABA-dependent components were found to, at least partly, to function as the systemic signal.

    Keywords
    aequorin, gene expression, HDZip, signal transduction
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-92028 (URN)10.1111/j.1365-3040.2004.01263.x (DOI)
    Available from: 2004-09-02 Created: 2004-09-02 Last updated: 2017-12-14Bibliographically approved
    3. The Arabidopsis homeobox gene, ATHB16, regulates leaf development and the sensitivity to photoperiod in Arabidopsis
    Open this publication in new window or tab >>The Arabidopsis homeobox gene, ATHB16, regulates leaf development and the sensitivity to photoperiod in Arabidopsis
    Show others...
    2003 (English)In: Developmental Biology, Vol. 264, p. 228-239Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92029 (URN)
    Available from: 2004-09-02 Created: 2004-09-02 Last updated: 2009-04-02Bibliographically approved
    4. The HDZip class I genes ATHB5, -6 and -16 act redundantly to mediate light effects on hypocotyl elongation
    Open this publication in new window or tab >>The HDZip class I genes ATHB5, -6 and -16 act redundantly to mediate light effects on hypocotyl elongation
    Show others...
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-92030 (URN)
    Available from: 2004-09-02 Created: 2004-09-02 Last updated: 2010-01-14Bibliographically approved
  • 12.
    Henriksson, Eva
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Nordin Henriksson, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Salt stress signalling and the role of calcium in the regulation of the Arabidopsis ATHB7 gene2005In: Plant, Cell and Environment, ISSN 0140-7791, E-ISSN 1365-3040, Vol. 28, no 2, p. 202-210Article in journal (Refereed)
    Abstract [en]

    In plants changes in cytosolic calcium ion concentrations ([Ca2+]cyt) have been detected after various stress treatments, including salt treatment. The involvement of a Ca2+ signal as an essential component of signalling pathways leading to downstream responses, such as gene expression, is supported only by a few studies. In this study the possible involvement of the salt stress-induced increase in [Ca2+]cyt in the signalling pathway leading to the induction of ATHB7, a homeobox gene encoding a homeodomain leucine zipper (HDZip) transcription factor was analysed. The salt-induced expression of ATHB7 was found to be independent of the Ca2+ signal evoked by salt. Instead, it was found that ATHB7 expression in shoots was not dependent on a direct contact with salt or osmoticum, whereas in roots, ATHB7 seemed to be induced by the direct contact, indicating that signals from roots cause systemic induction of ATHB7. Abscisic acid (ABA) or ABA-dependent components were found to, at least partly, to function as the systemic signal.

  • 13.
    Henriksson, Eva
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Nordin Henriksson, Kerstin
    Johannesson, Henrik
    Söderman, Eva
    Engström, Peter
    The HDZip class I genes ATHB5, -6 and -16 act redundantly to mediate light effects on hypocotyl elongationManuscript (Other (popular science, discussion, etc.))
  • 14.
    Henriksson, Eva
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Olsson, Anna
    Johannesson, Henrik
    Johansson, Henrik
    Hanson, Johannes
    Engström, Peter
    Söderman, Eva
    HDZip class I genes in Arabidopsis: expression profiles and phylogenetic relationshipsManuscript (Other (popular science, discussion, etc.))
  • 15.
    Henriksson, Eva
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Physiological Botany. fysiologisk botanik.
    Olsson, Anna
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Physiological Botany. fysiologisk botanik.
    Johannesson, Henrik
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Physiological Botany. fysiologisk botanik.
    Johansson, Henrik
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Hanson, Johannes
    Engström, Peter
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Physiological Botany. fysiologisk botanik.
    Söderman, Eva
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Physiological Botany. fysiologisk botanik.
    Homeodomain leucine zipper class I genes in Arabidopsis. Expression patterns and phylogenetic relationships2005In: Plant Physiology, ISSN 0032-0889, Vol. 139, no 1, p. 509-518Article in journal (Other (popular scientific, debate etc.))
    Abstract [en]

    Members of the homeodomain leucine zipper (HDZip) family of transcription factors are present in a wide range of plants, from mosses to higher plants, but not in other eukaryotes. The HDZip genes act in developmental processes, including vascular tissue and trichome development, and several of them have been suggested to be involved in the mediation of external signals to regulate plant growth. The Arabidopsis ( Arabidopsis thaliana) genome contains 47 HDZip genes, which, based on sequence criteria, have been grouped into four different classes: HDZip I to IV. In this article, we present an overview of the class I HDZip genes in Arabidopsis. We describe their expression patterns, transcriptional regulation properties, duplication history, and phylogeny. The phylogeny of HDZip class I genes is supported by data on the duplication history of the genes, as well as the intron/exon patterning of the HDZip-encoding motifs. The HDZip class I genes were found to be widely expressed and partly to have overlapping expression patterns at the organ level. Further, abscisic acid or water deficit treatments and different light conditions affected the transcript levels of a majority of the HDZip I genes. Within the gene family, our data show examples of closely related HDZip genes with similarities in the function of the gene product, but a divergence in expression pattern. In addition, six HDZip class I proteins tested were found to be activators of gene expression. In conclusion, several HDZip I genes appear to regulate similar cellular processes, although in different organs or tissues and in response to different environmental signals.

  • 16. Henriksson, Eva
    et al.
    Olsson, Anna S. B.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Johannesson, Henrik
    Johansson, Henrik
    Hanson, Johannes
    Engström, Peter
    Söderman, Eva
    Class I HDZip genes in Arabidopsis: expression patterns and phylogenyManuscript (Other (popular science, discussion, etc.))
  • 17. Hjellström, Mattias
    et al.
    Olsson, Anna S. B.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Engström, Peter
    Söderman, Eva
    Constitutive expression of the water deficit-inducible homeobox gene ATHB7 in transgenic Arabidopsis causes a suppression of stem elongation growth2003In: Plant, Cell and Environment, ISSN 0140-7791, no 26, p. 1127-1136Article in journal (Refereed)
  • 18. Kuijt, Suzanne J. H.
    et al.
    Greco, Raffaella
    Agalou, Adamantia
    Shao, Jingxia
    't Hoen, Corine C. J.
    Övernas, Elin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Osnato, Michela
    Curiale, Serena
    Meynard, Donaldo
    van Gulik, Robert
    Maraschin, Simone de Faria
    Atallah, Mirna
    de Kam, Rolf J.
    Lamers, Gerda E. M.
    Guiderdoni, Emmanuel
    Rossini, Laura
    Meijer, Annemarie H.
    Ouwerkerk, Pieter B. F.
    Interaction between the GROWTH-REGULATING FACTOR and KNOTTED1-LIKE HOMEOBOX Families of Transcription Factors1[W]2014In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 164, no 4, p. 1952-1966Article in journal (Refereed)
    Abstract [en]

    KNOTTED1-LIKE HOMEOBOX (KNOX) genes are important regulators of meristem function, and a complex network of transcription factors ensures tight control of their expression. Here, we show that members of the GROWTH-REGULATING FACTOR (GRF) family act as players in this network. A yeast (Saccharomyces cerevisiae) one-hybrid screen with the upstream sequence of the KNOX gene Oskn2 from rice (Oryza sativa) resulted in isolation of OsGRF3 and OsGRF10. Specific binding to a region in the untranslated leader sequence of Oskn2 was confirmed by yeast and in vitro binding assays. ProOskn2: beta-glucuronidase reporter expression was down-regulated by OsGRF3 and OsGRF10 in vivo, suggesting that these proteins function as transcriptional repressors. Likewise, we found that the GRF protein BGRF1 from barley (Hordeum vulgare) could act as a repressor on an intron sequence in the KNOX gene Hooded/Barley Knotted3 (Bkn3) and that AtGRF4, AtGRF5, and AtGRF6 from Arabidopsis (Arabidopsis thaliana) could repress KNOTTED-LIKE FROM ARABIDOPSIS THALIANA2 (KNAT2) promoter activity. OsGRF overexpression phenotypes in rice were consistent with aberrant meristematic activity, showing reduced formation of tillers and internodes and extensive adventitious root/shoot formation on nodes. These effects were associated with down-regulation of endogenous Oskn2 expression by OsGRF3. Conversely, RNA interference silencing of OsGRF3, OsGRF4, and OsGRF5 resulted in dwarfism, delayed growth and inflorescence formation, and up-regulation of Oskn2. These data demonstrate conserved interactions between the GRF and KNOX families of transcription factors in both monocot and dicot plants.

  • 19.
    Landberg, Katarina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    TERMINAL FLOWER2, the Arabidopsis HETEROCHROMATIN PROTEIN1 Homolog, and its Involvement in Plant Development2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis describes the characterization of the Arabidopsis thaliana mutant terminal flower2 (tfl2), the cloning of the corresponding gene, and the analysis of TFL2 function in plant development. The tfl2 mutant is pleiotropic, exhibiting early floral induction in both long and short day conditions, a terminating inflorescence and dwarfing. TFL2 was isolated using a positional cloning strategy, and was found to encode a homolog to HETEROCHROMATIN PROTEIN1 (HP1), previously identified in yeast and animals where it is involved in gene regulation at the level of chromatin, as well as in the structural formation of constitutive heterochromatin.

    Investigating the light response during seedling photomorphogenesis I found that the tfl2 hypocotyl is hypersensitive to red and far-red light and that tfl2 is impaired in phytochrome mediated light responses such as the shade avoidance response. In the tightly regulated transition to flowering, we have shown that tfl2 might contribute to the interpretation of both external signals such as light and temperature as well as endogenous cues, via FCA, in the autonomous pathway. The Arabidopsis inflorescence meristem is indeterminate, and TFL2 possibly acts to maintain this indeterminate fate by repression of the floral meristem genes APETALA1 and AGAMOUS. In yeast two hybrid experiments TFL2 was shown to interact with IAA5, a protein with suggested functions in auxin regulation. Further, in tfl2 mutants the levels of the auxin indole-3-acetic acid decrease with age in aerial tissues, suggesting a function of TFL2 in regulation of auxin homeostasis and response. In summary, TFL2 contributes to regulation of several aspects of plant development, in accordance with the mutant phenotype and the identity of the TFL2 protein.

    List of papers
    1. The TERMINAL FLOWER2 (TFL2) gene controls the reproductive transition and meristem identity in Arabidopsis thaliana
    Open this publication in new window or tab >>The TERMINAL FLOWER2 (TFL2) gene controls the reproductive transition and meristem identity in Arabidopsis thaliana
    1998 (English)In: Genetics, Vol. 149, no 2, p. 597-605Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-95462 (URN)
    Available from: 2007-02-22 Created: 2007-02-22 Last updated: 2009-04-02Bibliographically approved
    2. TERMINAL FLOWER2 (TFL2) regulates the transition to flowering through the autonomous pathway
    Open this publication in new window or tab >>TERMINAL FLOWER2 (TFL2) regulates the transition to flowering through the autonomous pathway
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-95463 (URN)
    Available from: 2007-02-22 Created: 2007-02-22 Last updated: 2010-01-14Bibliographically approved
    3. TERMINAL FLOWER2, the Arabidopsis HP1 protein, is involved in light-controlled signaling during seedling photomorphogenesis
    Open this publication in new window or tab >>TERMINAL FLOWER2, the Arabidopsis HP1 protein, is involved in light-controlled signaling during seedling photomorphogenesis
    Show others...
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-95464 (URN)
    Available from: 2007-02-22 Created: 2007-02-22 Last updated: 2010-01-14Bibliographically approved
    4. TERMINAL FLOWER2 regulates auxin levels and auxin response in Arabidopsis
    Open this publication in new window or tab >>TERMINAL FLOWER2 regulates auxin levels and auxin response in Arabidopsis
    Show others...
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-95465 (URN)
    Available from: 2007-02-22 Created: 2007-02-22 Last updated: 2010-01-14Bibliographically approved
  • 20.
    Landberg, Katarina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Johannesson, Henrik
    Para, Alessia
    Nilsson, Lars
    Sundås Larsson, Annika
    TERMINAL FLOWER2, the Arabidopsis HP1 protein, is involved in light-controlled signaling during seedling photomorphogenesisManuscript (Other (popular science, discussion, etc.))
  • 21. Landberg, Katarina
    et al.
    Nilsson, Lars
    Para, Alessia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Sundås Larsson, Annika
    The TERMINAL FLOWER2 (TFL2) Gene Regulates the Transition to Flowering by Repressing Gene ActivityManuscript (Other (popular science, discussion, etc.))
  • 22.
    Landberg, Katarina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Nilsson, Lars
    Rizzardi, Kristina
    Ljung, Karin
    Sundås Larsson, Annika
    TERMINAL FLOWER2 regulates auxin levels and auxin response in ArabidopsisManuscript (Other (popular science, discussion, etc.))
  • 23. Landberg, Katarina
    et al.
    Nilsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Rizzardi, Kristina
    Ljung, Karin
    Sundås Larsson, Annika
    TERMINAL FLOWER2 regulates auxin levels and auxin response in ArabidopsisManuscript (Other (popular science, discussion, etc.))
  • 24.
    Landberg, Katarina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Nilsson, Lars
    Sundås Larsson, Annika
    TERMINAL FLOWER2 (TFL2) regulates the transition to flowering through the autonomous pathwayManuscript (Other (popular science, discussion, etc.))
  • 25. Landberg, Katarina
    et al.
    Nilsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Sundås Larsson, Annika
    (TFL2) Regulates the Transition to Flowering Through the Autonomous PathwayManuscript (Other (popular science, discussion, etc.))
  • 26. Lehtilä, Kari
    et al.
    Sundås Larsson, Annika
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Physiological Botany. Fysiologisk botanik.
    Meristem Allocation as a Means of Assessing Reproductive Allocation2005In: Reproductive Allocation in Plants, Elsevier, Amsterdam, Boston, Heidelberg, London, New York, Oxford, Paris, San Diego, San Fransisco, Singapore, Sydney, Tokyo , 2005, p. 51-75Chapter in book (Other (popular scientific, debate etc.))
  • 27.
    Lindberg, Pia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany. Fysiologisk botanik.
    Lindblad, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany. Fysiologisk botanik.
    Cournac, Laurent
    Gas Exchange in the Filamentous Cyanobacterium Nostoc punctiforme Strain ATCC 29133 and Its Hydrogenase-Deficient Mutant Strain NHM52004In: Applied and Environmental Microbiology, Vol. 70, no 4, p. 2137-2145Article in journal (Refereed)
    Abstract [en]

    Nostoc punctiforme ATCC 29133 is a nitrogen-fixing, heterocystous cyanobacterium of symbiotic origin. During nitrogen fixation, it produces molecular hydrogen (H2), which is recaptured by an uptake hydrogenase. Gas exchange in cultures of N. punctiforme ATCC 29133 and its hydrogenase-free mutant strain NHM5 was studied. Exchange of O2, CO2, N2 and H2 was followed simultaneously with mass spectrometer in cultures grown under nitrogen-fixing conditions. Isotopic tracing was used to separate evolution and uptake of CO2 and O2. The amount of H2 produced per molecule of N2 fixed was found to vary with light conditions, high light giving a greater increase in H2 production than N2 fixation. The ratio under low light and high light was approximately 1.4 and 6.1 molecules of H2 produced per molecule of N2 fixed, respectively. Incubation under high light for a longer time, until the culture was depleted of CO2, caused a decrease in the nitrogen fixation rate. At the same time, hydrogen production in the hydrgenase-deficient strain was increased from an initial rate of approximately 6 umol (mg of chlorophyll a)-1h-1 to 9 umol (mg of chlorophyll a)-1h-1 after about 50 min. A light-stimulated hydrogen-deuterium exchange activity stemming from the nitrogenase was observed in the two strains. The present findings are important for understanding this nitrogenase-based system, aiming at photobiological hydrogen production, as we have identified the conditions under which the energy flow through the nitrogenase can be directed towards hydrogen production rather than nitrogen fixation.

  • 28.
    Lopes Pinto, Fernando
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Svensson, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Lindblad, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Generation of non-genomic oligonucleotide tag sequences for RNA template-specific PCR2006In: BMC Biotechnology, ISSN 1472-6750, E-ISSN 1472-6750, Vol. 6, p. 31-Article in journal (Refereed)
    Abstract [en]

    Background

    In order to overcome genomic DNA contamination in transcriptional studies, reverse template-specific polymerase chain reaction, a modification of reverse transcriptase polymerase chain reaction, is used. The possibility of using tags whose sequences are not found in the genome further improves reverse specific polymerase chain reaction experiments. Given the absence of software available to produce genome suitable tags, a simple tool to fulfill such need was developed.

    Results

    The program was developed in Perl, with separate use of the basic local alignment search tool, making the tool platform independent (known to run on Windows XP and Linux). In order to test the performance of the generated tags, several molecular experiments were performed. The results show that Tagenerator is capable of generating tags with good priming properties, which will deliberately not result in PCR amplification of genomic DNA.

    Conclusion

    The program Tagenerator is capable of generating tag sequences that combine genome absence with good priming properties for RT-PCR based experiments, circumventing the effects of genomic DNA contamination in an RNA sample.

  • 29.
    Nilsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Analysis of Two Transcriptional Regulators that Affect Meristem Function: Arabidopsis thaliana TERMINAL FLOWER2 and Picea abies APETELA22007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The aerial plant body is derived from undifferentiated cells in the shoot apical meristem that in Arabidopsis thaliana is active throughout the plant life cycle. Upon transition to flowering the activity of the meristem is altered and the meristem starts to produce secondary inflorescences and floral meristems instead of leaves. Both the activity of the meristem and the decision of when to flower are processes strictly regulated by several mechanisms. In this thesis I describe the function of two genes that are active in the regulation of meristem function and in the regulation of when to shift to reproductive development.

    First, the Arabidopsis gene encoding TERMINAL FLOWER2 (TFL2), homologous to HETEROCHROMATIN PROTEIN1, was isolated and characterised. Mutations in TFL2 result in plants that are dwarfed, flowers early, have reduced sensitivity to day length and terminate the inflorescence in an apical flower. As homologues from other organisms TFL2 is active in gene regulation by gene repression. I show that the gene affect flowering time by the autonomous and the photoperiod pathways, two of four floral inductive pathways. TFL2 act to repress the activity of genes that are promoters of floral meristem identity and interacts genetically with factors known to alter the chromatin state. Further tfl2 is shown to have altered levels of and response to auxin. All together this shows that TFL2 is active as a regulator of several different processes during plant development.

    Second, I have characterised and studied the function of three genes encoding APETALA2 LIKE proteins in Norway spruce (Picea abies). In spruce these genes are expressed in meristems and reproductive tissues. When constitutively expressed in Arabidopsis two of the genes delays flowering time and alter the function of shoot apical and floral meristems. Together this suggests a function similar to the Arabidopsis homologues.

    List of papers
    1. (TFL2) Regulates the Transition to Flowering Through the Autonomous Pathway
    Open this publication in new window or tab >>(TFL2) Regulates the Transition to Flowering Through the Autonomous Pathway
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-95345 (URN)
    Available from: 2007-01-11 Created: 2007-01-11 Last updated: 2010-01-14Bibliographically approved
    2. Homeotic gene expression is regulated by TERMINAL FLOWER2 and the CAF-1 complex
    Open this publication in new window or tab >>Homeotic gene expression is regulated by TERMINAL FLOWER2 and the CAF-1 complex
    Show others...
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-95346 (URN)
    Available from: 2007-01-11 Created: 2007-01-11 Last updated: 2010-01-14Bibliographically approved
    3. TERMINAL FLOWER2 regulates auxin levels and auxin response in Arabidopsis
    Open this publication in new window or tab >>TERMINAL FLOWER2 regulates auxin levels and auxin response in Arabidopsis
    Show others...
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-95347 (URN)
    Available from: 2007-01-11 Created: 2007-01-11 Last updated: 2010-01-14Bibliographically approved
    4. APETALA2 like genes from Picea abies show functional similarities to their Arabidopsis homologues
    Open this publication in new window or tab >>APETALA2 like genes from Picea abies show functional similarities to their Arabidopsis homologues
    2007 (English)In: Planta, ISSN 0032-0935, E-ISSN 1432-2048, Vol. 225, no 3, p. 589-602Article in journal (Refereed) Published
    Abstract [en]

    In angiosperm flower development the identity of the floral organs is determined by the A, B and C factors. Here we present the characterisation of three homologues of the A class gene APETALA2 (AP2) from the conifer Picea abies (Norway spruce), Picea abies APETALA2 LIKE1 (PaAP2L1), PaAP2L2 and PaAP2L3. Similar to AP2 these genes contain sequence motifs complementary to miRNA172 that has been shown to regulate AP2 in Arabidopsis. The genes display distinct expression patterns during plant development; in the female-cone bud PaAP2L1 and PaAP2L3 are expressed in the seed-bearing ovuliferous scale in a pattern complementary to each other, and overlapping with the expression of the C class-related gene DAL2. To study the function of PaAP2L1 and PaAP2L2 the genes were expressed in Arabidopsis. The transgenic PaAP2L2 plants were stunted and flowered later than control plants. Flowers were indeterminate and produced an excess of floral organs most severely in the two inner whorls, associated with an ectopic expression of the meristem-regulating gene WUSCHEL. No homeotic changes in floral-organ identities occurred, but in the ap2-1 mutant background PaAP2L2 was able to promote petal identity, indicating that the spruce AP2 gene has the capacity to substitute for an A class gene in Arabidopsis. In spite of the long evolutionary distance between angiosperms and gymnosperms and the fact that gymnosperms lack structures homologous to sepals and petals our data supports a functional conservation of AP2 genes among the seed plants.

    Keywords
    APETALA2, Flowering time, Meristem maintenance, microRNA, Picea abies
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-95348 (URN)10.1007/s00425-006-0374-1 (DOI)000243964000006 ()16953432 (PubMedID)
    Available from: 2007-01-11 Created: 2007-01-11 Last updated: 2017-12-14Bibliographically approved
  • 30.
    Nilsson, Lars
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Landberg, Katarina
    Rizzardi, Kristina
    Para, Alessia
    Sundås Larsson, Annika
    Homeotic gene expression is regulated by TERMINAL FLOWER2 and the CAF-1 complexManuscript (Other (popular science, discussion, etc.))
  • 31.
    Olsson, Anna S. B.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    HDZip I Transcription Factors in Arabidopsis thaliana: Expression and Function in Relation to Environmental Stress Conditions2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The homeodomain leucine zipper (HDZip) proteins constitute a plant-specific family of transcription factors, that based on sequence criteria have been grouped into four classes, HDZip I-IV. This thesis describes the phylogeny, function, expression patterns and regulation of the HDZip class I genes in the model species Arabidopsis thaliana.

    The phylogenetic analyses, traced duplication history and exon/intron organisation of the 17 class I genes in Arabidopsis show that the genes form six monophyletic groups, clades, with an origin in early plant evolution. All genes are expressed in broad tissue distribution patterns and the majority are responsive to water availability and/or light conditions. The expression of the genes show different patterns and dependence on environmental stress conditions, indicating evolutionary changes within and between clades. Ectopic expression of the genes suggest that they regulate genes in part by conserved mechanisms. Therefore, different functional roles seem to have evolved by a divergence mainly in the regulatory properties of the genes.

    Detailed expression analyses of the paralogous HDZip I genes ATHB7 and ATHB12 show that they have essentially overlapping patterns of activity in response to abscisic acid, ABA, or water deficit in leaves, stems and roots. The water deficit response of ATHB7 and -12 is mediated by ABA and depends on the protein phosphateses ABI1 and ABI2. Transgenic plants with ectopic expression of ATHB7 and/or -12, and athb7 and athb12 mutants, reveal that the genes in roots mediate the growth inhibitory effects of ABA. In this aspect of their function they do not overlap. In leaves and stems, the genes might act as growth regulators redundantly with other factors.

    Taken together these data suggest that ATHB7 and -12 regulate growth in response water deficit and that other HDZip I genes have related functions in response to environmental stress conditions.

    List of papers
    1. Class I HDZip genes in Arabidopsis: expression patterns and phylogeny
    Open this publication in new window or tab >>Class I HDZip genes in Arabidopsis: expression patterns and phylogeny
    Show others...
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-92617 (URN)
    Available from: 2005-02-21 Created: 2005-02-21 Last updated: 2010-01-14Bibliographically approved
    2. Constitutive expression of the water deficit-inducible homeobox gene ATHB7 in transgenic Arabidopsis causes a suppression of stem elongation growth
    Open this publication in new window or tab >>Constitutive expression of the water deficit-inducible homeobox gene ATHB7 in transgenic Arabidopsis causes a suppression of stem elongation growth
    2003 (English)In: Plant, Cell and Environment, ISSN 0140-7791, no 26, p. 1127-1136Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92618 (URN)
    Available from: 2005-02-21 Created: 2005-02-21 Last updated: 2009-04-02Bibliographically approved
    3. The homeobox genes ATHB12 and ATHB7 encode potential regulators of growth in response to water deficit in Arabidopsis
    Open this publication in new window or tab >>The homeobox genes ATHB12 and ATHB7 encode potential regulators of growth in response to water deficit in Arabidopsis
    2004 (English)In: Plant Molecular Biology, ISSN 0167-4412, no 55, p. 663-677Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92619 (URN)