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Bako, Laszlo
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Publications (10 of 23) Show all publications
Chahtane, H., Zhang, B., Norberg, M., LeMasson, M., Thevenon, E., Bakó, L., . . . Vachon, G. (2018). LEAFY activity is post-transcriptionally regulated by BLADE ON PETIOLE2 and CULLIN3 in Arabidopsis. New Phytologist, 220(2), 579-592
Open this publication in new window or tab >>LEAFY activity is post-transcriptionally regulated by BLADE ON PETIOLE2 and CULLIN3 in Arabidopsis
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2018 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 220, no 2, p. 579-592Article in journal (Refereed) Published
Abstract [en]

The Arabidopsis LEAFY (LFY) transcription factor is a key regulator of floral meristem emergence and identity. LFY interacts genetically and physically with UNUSUAL FLORAL ORGANS, a substrate adaptor of CULLIN1-RING ubiquitin ligase complexes (CRL1). The functionally redundant genes BLADE ON PETIOLE1 (BOP1) and -2 (BOP2) are potential candidates to regulate LFY activity and have recently been shown to be substrate adaptors of CULLIN3 (CUL3)-RING ubiquitin ligases (CRL3). We tested the hypothesis that LFY activity is controlled by BOPs and CUL3s in plants and that LFY is a substrate for ubiquitination by BOP-containing CRL3 complexes. When constitutively expressed, LFY activity is fully dependent on BOP2 as well as on CUL3A and B to regulate target genes such as APETALA1 and to induce ectopic flower formation. We also show that LFY and BOP2 proteins interact physically and that LFY-dependent ubiquitinated species are produced invitro in a reconstituted cell-free CRL3 system in the presence of LFY, BOP2 and CUL3. This new post-translational regulation of LFY activity by CRL3 complexes makes it a unique transcription factor subjected to a positive dual regulation by both CRL1 and CRL3 complexes and suggests a novel mechanism for promoting flower development.

Place, publisher, year, edition, pages
Wiley-Blackwell, 2018
Keywords
BLADE-ON-PETIOLE, cullin 3, flower development, inflorescence, LEAFY, post-transcriptional regulation, ubiquitination
National Category
Environmental Sciences
Identifiers
urn:nbn:se:umu:diva-152392 (URN)10.1111/nph.15329 (DOI)000445194100022 ()29995985 (PubMedID)
Projects
Bio4Energy
Funder
The Kempe Foundations
Available from: 2018-10-08 Created: 2018-10-08 Last updated: 2019-09-06Bibliographically approved
Caballero-Pérez, J., Espinal-Centeno, A., Falcon, F., García-Ortega, L. F., Curiel-Quesada, E., Cruz-Hernández, A., . . . Cruz-Ramírez, A. (2018). Transcriptional landscapes of Axolotl (Ambystoma mexicanum). Developmental Biology, 433(2), 227-239
Open this publication in new window or tab >>Transcriptional landscapes of Axolotl (Ambystoma mexicanum)
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2018 (English)In: Developmental Biology, ISSN 0012-1606, E-ISSN 1095-564X, Vol. 433, no 2, p. 227-239Article in journal (Refereed) Published
Abstract [en]

The axolotl (Ambystoma mexicanum) is the vertebrate model system with the highest regeneration capacity. Experimental tools established over the past 100 years have been fundamental to start unraveling the cellular and molecular basis of tissue and limb regeneration. In the absence of a reference genome for the Axolotl, transcriptomic analysis become fundamental to understand the genetic basis of regeneration.

Here we present one of the most diverse transcriptomic data sets for Axolotl by profiling coding and non coding RNAs from diverse tissues. We reconstructed a population of 115,906 putative protein coding mRNAs as full ORFs (including isoforms). We also identified 352 conserved miRNAs and 297 novel putative mature miRNAs.

Systematic enrichment analysis of gene expression allowed us to identify tissue-specific protein-coding transcripts. We also found putative novel and conserved microRNAs which potentially target mRNAs which are reported as important disease candidates in heart and liver.

Place, publisher, year, edition, pages
Elsevier, 2018
Keywords
coding and non-coding RNAseq, axolotl, regenerative tissues, microRNAs
National Category
Bioinformatics and Systems Biology Developmental Biology
Identifiers
urn:nbn:se:umu:diva-144842 (URN)10.1016/j.ydbio.2017.08.022 (DOI)000423009700014 ()29291975 (PubMedID)
Available from: 2018-02-23 Created: 2018-02-23 Last updated: 2018-06-09Bibliographically approved
Zhang, B., Holmlund, M., Lorrain, S., Norberg, M., Bakó, L., Fankhauser, C. & Nilsson, O. (2017). BLADE-ON-PETIOLE proteins act in an E3 ubiquitin ligase complex to regulate PHYTOCHROME INTERACTING FACTOR 4 abundance. eLIFE, 6, Article ID e26759.
Open this publication in new window or tab >>BLADE-ON-PETIOLE proteins act in an E3 ubiquitin ligase complex to regulate PHYTOCHROME INTERACTING FACTOR 4 abundance
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2017 (English)In: eLIFE, E-ISSN 2050-084X, Vol. 6, article id e26759Article in journal (Refereed) Published
Abstract [en]

Both light and temperature have dramatic effects on plant development. Phytochrome photoreceptors regulate plant responses to the environment in large part by controlling the abundance of PHYTOCHROME INTERACTING FACTOR (PIF) transcription factors. However, the molecular determinants of this essential signaling mechanism still remain largely unknown. Here, we present evidence that the BLADE-ON-PETIOLE (BOP) genes, which have previously been shown to control leaf and flower development in Arabidopsis, are involved in controlling the abundance of PIF4. Genetic analysis shows that BOP2 promotes photo-morphogenesis and modulates thermomorphogenesis by suppressing PIF4 activity, through a reduction in PIF4 protein level. In red-light-grown seedlings PIF4 ubiquitination was reduced in the bop2 mutant. Moreover, we found that BOP proteins physically interact with both PIF4 and CULLIN3A and that a CULLIN3-BOP2 complex ubiquitinates PIF4 in vitro. This shows that BOP proteins act as substrate adaptors in a CUL3BOP1/BOP2 E3 ubiquitin ligase complex, targeting PIF4 proteins for ubiquitination and subsequent degradation.

Place, publisher, year, edition, pages
eLife Sciences Publications, Ltd, 2017
National Category
Developmental Biology
Identifiers
urn:nbn:se:umu:diva-139145 (URN)10.7554/eLife.26759 (DOI)000408089600001 ()
Projects
Bio4Energy
Available from: 2017-10-03 Created: 2017-10-03 Last updated: 2019-09-06Bibliographically approved
Concepcion Cruz-Santos, M., Aragon-Raygoza, A., Espinal-Centeno, A., Arteaga-Vazquez, M., Cruz-Hernandez, A., Bako, L. & Cruz-Ramirez, A. (2016). The Role of microRNAs in Animal Cell Reprogramming. Stem Cells and Development, 25(14), 1035-1049
Open this publication in new window or tab >>The Role of microRNAs in Animal Cell Reprogramming
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2016 (English)In: Stem Cells and Development, ISSN 1547-3287, E-ISSN 1557-8534, Vol. 25, no 14, p. 1035-1049Article, review/survey (Refereed) Published
Abstract [en]

Our concept of cell reprogramming and cell plasticity has evolved since John Gurdon transferred the nucleus of a completely differentiated cell into an enucleated Xenopus laevis egg, thereby generating embryos that developed into tadpoles. More recently, induced expression of transcription factors, oct4, sox2, klf4, and c-myc has evidenced the plasticity of the genome to change the expression program and cell phenotype by driving differentiated cells to the pluripotent state. Beyond these milestone achievements, research in artificial cell reprogramming has been focused on other molecules that are different than transcription factors. Among the candidate molecules, microRNAs (miRNAs) stand out due to their potential to control the levels of proteins that are involved in cellular processes such as self-renewal, proliferation, and differentiation. Here, we review the role of miRNAs in the maintenance and differentiation of mesenchymal stem cells, epimorphic regeneration, and somatic cell reprogramming to induced pluripotent stem cells.

National Category
Cell Biology
Identifiers
urn:nbn:se:umu:diva-124325 (URN)10.1089/scd.2015.0359 (DOI)000379611100001 ()27224014 (PubMedID)
External cooperation:
Available from: 2016-09-07 Created: 2016-08-04 Last updated: 2018-06-07Bibliographically approved
Le Hir, R., Sorin, C., Chakraborti, D., Moritz, T., Schaller, H., Tellier, F., . . . Bellini, C. (2013). ABCG9, ABCG11 and ABCG14 ABC transporters are required for vascular development in Arabidopsis. The Plant Journal, 76(5), 811-824
Open this publication in new window or tab >>ABCG9, ABCG11 and ABCG14 ABC transporters are required for vascular development in Arabidopsis
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2013 (English)In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 76, no 5, p. 811-824Article in journal (Refereed) Published
Abstract [en]

In order to obtain insights into the regulatory pathways controlling phloem development, we characterized three genes encoding membrane proteins from the G sub-family of ABC transporters (ABCG9, ABCG11 and ABCG14), whose expression in the phloem has been confirmed. Mutations in the genes encoding these dimerizing half transporters' are semi-dominant and result in vascular patterning defects in cotyledons and the floral stem. Co-immunoprecipitation and bimolecular fluorescence complementation experiments demonstrated that these proteins dimerize, either by flexible pairing (ABCG11 and ABCG9) or by forming strict heterodimers (ABCG14). In addition, metabolome analyses and measurement of sterol ester contents in the mutants suggested that ABCG9, ABCG11 and ABCG14 are involved in lipid/sterol homeostasis regulation. Our results show that these three ABCG genes are required for proper vascular development in Arabidopsis thaliana.

Place, publisher, year, edition, pages
Wiley-Blackwell, 2013
Keywords
vascular development, ABC transporters, ABCG dimer, lipid, sterol homeostasis, Arabidopsis thaliana
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-85557 (URN)10.1111/tpj.12334 (DOI)000327511600008 ()
Funder
Swedish Research CouncilSwedish Foundation for Strategic Research Knut and Alice Wallenberg FoundationCarl Tryggers foundation
Available from: 2014-02-07 Created: 2014-02-06 Last updated: 2018-06-08Bibliographically approved
Cruz-Ramírez, A., Díaz-Triviño, S., Blilou, I., Grieneisen, V. A., Sozzani, R., Zamioudis, C., . . . Scheres, B. (2012). A Bistable Circuit Involving SCARECROW-RETINOBLASTOMA Integrates Cues to Inform Asymmetric Stem Cell Division. Cell, 150(5), 1002-1015
Open this publication in new window or tab >>A Bistable Circuit Involving SCARECROW-RETINOBLASTOMA Integrates Cues to Inform Asymmetric Stem Cell Division
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2012 (English)In: Cell, ISSN 0092-8674, E-ISSN 1097-4172, Vol. 150, no 5, p. 1002-1015Article in journal (Refereed) Published
Abstract [en]

In plants, where cells cannot migrate, asymmetric cell divisions (ACDs) must be confined to the appropriate spatial context. We investigate tissue-generating asymmetric divisions in a stem cell daughter within the Arabidopsis root. Spatial restriction of these divisions requires physical binding of the stem cell regulator SCARECROW (SCR) by the RETINOBLASTOM-RELATED (RBR) protein. In the stem cell niche, SCR activity is counteracted by phosphorylation of RBR through a cyclinD6;1-CDK complex. This cyclin is itself under transcriptional control of SCR and its partner SHORT ROOT (SHR), creating a robust bistable circuit with either high or low SHR-SCR complex activity. Auxin biases this circuit by promoting CYCD6;1 transcription. Mathematical modeling shows that ACDs are only switched on after integration of radial and longitudinal information, determined by SHR and auxin distribution, respectively. Coupling of cell-cycle progression to protein degradation resets the circuit, resulting in a "flip flop" that constrains asymmetric cell division to the stem cell region.

Place, publisher, year, edition, pages
Elsevier, 2012
National Category
Biochemistry and Molecular Biology Cell Biology
Identifiers
urn:nbn:se:umu:diva-104253 (URN)10.1016/j.cell.2012.07.017 (DOI)000308500200014 ()22921914 (PubMedID)
Available from: 2015-06-10 Created: 2015-06-09 Last updated: 2018-06-07Bibliographically approved
Magyar, Z., Horvath, B., Khan, S., Mohammed, B., Henriques, R., De Veylder, L., . . . Boegre, L. (2012). Arabidopsis E2FA stimulates proliferation and endocycle separately through RBR-bound and RBR-free complexes. EMBO Journal, 31(6), 1480-1493
Open this publication in new window or tab >>Arabidopsis E2FA stimulates proliferation and endocycle separately through RBR-bound and RBR-free complexes
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2012 (English)In: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 31, no 6, p. 1480-1493Article in journal (Refereed) Published
Abstract [en]

Post-embryonic growth in plants depends on the continuous supply of undifferentiated cells within meristems. Proliferating cells maintain their competence for division by active repression of differentiation and the associated endocycle entry. We show by upregulation and downregulation of E2FA that it is required for maintaining proliferation, as well as for endocycle entry. While E2FB-RBR1 (retinoblastoma-related protein 1) complexes are reduced after sucrose addition or at elevated CYCD3;1 levels, E2FA maintains a stable complex with RBR1 in proliferating cells. Chromatin immunoprecipitation shows that RBR1 binds in the proximity of E2F promoter elements in CCS52A1 and CSS52A2 genes, central regulators for the switch from proliferation to endocycles. Overexpression of a truncated E2FA mutant (E2FA(Delta RB)) lacking the RBR1-binding domain interferes with RBR1 recruitment to promoters through E2FA, leading to decreased meristem size in roots, premature cell expansion and hyperactivated endocycle in leaves. E2F target genes, including CCS52A1 and CCS52A2, are upregulated in E2FADRB and e2fa knockout lines. These data suggest that E2FA in complex with RBR1 forms a repressor complex in proliferating cells to inhibit premature differentiation and endocycle entry. Thus, E2FA regulates organ growth via two distinct, sequentially operating pathways. The EMBO Journal (2012) 31, 1480-1493. doi:10.1038/emboj.2012.13; Published online 3 February 2012

Place, publisher, year, edition, pages
New York, NY, USA: Nature Publishing Group, 2012
Keywords
Arabidopsis, cell proliferation, endocycle, E2F, retinoblastoma
National Category
Biochemistry and Molecular Biology Cell Biology
Identifiers
urn:nbn:se:umu:diva-54327 (URN)10.1038/emboj.2012.13 (DOI)000302131600013 ()
Available from: 2012-04-24 Created: 2012-04-24 Last updated: 2018-06-08Bibliographically approved
Shaikhali, J., Barajas-Lopez, J. d., Ötvös, K., Kremnev, D., Garcia, A. S., Srivastava, V., . . . Strand, Å. (2012). The CRYPTOCHROME1-Dependent Response to Excess Light Is Mediated through the Transcriptional Activators ZINC FINGER PROTEIN EXPRESSED IN INFLORESCENCE MERISTEM LIKE1 and ZML2 in Arabidopsis. The Plant Cell, 24(7), 3009-3025
Open this publication in new window or tab >>The CRYPTOCHROME1-Dependent Response to Excess Light Is Mediated through the Transcriptional Activators ZINC FINGER PROTEIN EXPRESSED IN INFLORESCENCE MERISTEM LIKE1 and ZML2 in Arabidopsis
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2012 (English)In: The Plant Cell, ISSN 1040-4651, E-ISSN 1532-298X, Vol. 24, no 7, p. 3009-3025Article in journal (Refereed) Published
Abstract [en]

Exposure of plants to light intensities that exceed the electron utilization capacity of the chloroplast has a dramatic impact on nuclear gene expression. The photoreceptor Cryptochrome 1 (cry1) is essential to the induction of genes encoding photoprotective components in Arabidopsis thaliana. Bioinformatic analysis of the cry1 regulon revealed the putative ciselement CryR1 (GnTCKAG), and here we demonstrate an interaction between CryR1 and the zinc finger GATA-type transcription factors ZINC FINGER PROTEIN EXPRESSED IN INFLORESCENCE MERISTEM LIKE1 (ZML1) and ZML2. The ZML proteins specifically bind to the CryR1 cis-element as demonstrated in vitro and in vivo, and TCTAG was shown to constitute the core sequence required for ZML2 binding. In addition, ZML2 activated transcription of the yellow fluorescent protein reporter gene driven by the CryR1 cis-element in Arabidopsis leaf protoplasts. T-DNA insertion lines for ZML2 and its homolog ZML1 demonstrated misregulation of several cry1-dependent genes in response to excess light. Furthermore, the zml1 and zml2 T-DNA insertion lines displayed a high irradiance-sensitive phenotype with significant photoinactivation of photosystem II (PSII), indicated by reduced maximum quantum efficiency of PSII, and severe photobleaching. Thus, we identified the ZML2 and ZML1 GATA transcription factors as two essential components of the cry1-mediated photoprotective response.

National Category
Biological Sciences
Identifiers
urn:nbn:se:umu:diva-61232 (URN)10.1105/tpc.112.100099 (DOI)000308352800024 ()
Available from: 2012-11-07 Created: 2012-11-07 Last updated: 2018-06-08Bibliographically approved
Buren, S., Ortega-Villasante, C., Ötvös, K., Samuelsson, G., Bako, L. & Villarejo, A. (2012). Use of the foot-and-mouth disease virus 2A peptide co-expression system to study intracellular protein trafficking in arabidopsis. PLoS ONE, 7(12), e51973
Open this publication in new window or tab >>Use of the foot-and-mouth disease virus 2A peptide co-expression system to study intracellular protein trafficking in arabidopsis
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2012 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 12, p. e51973-Article in journal (Refereed) Published
Abstract [en]

Background: A tool for stoichiometric co-expression of effector and target proteins to study intracellular protein trafficking processes has been provided by the so called 2A peptide technology. In this system, the 16-20 amino acid 2A peptide from RNA viruses allows synthesis of multiple gene products from single transcripts. However, so far the use of the 2A technology in plant systems has been limited.

Methodology/Principal Findings: The aim of this work was to assess the suitability of the 2A peptide technology to study the effects exerted by dominant mutant forms of three small GTPase proteins, RABD2a, SAR1, and ARF1 on intracellular protein trafficking in plant cells. Special emphasis was given to CAH1 protein from Arabidopsis, which is trafficking to the chloroplast via a poorly characterized endoplasmic reticulum-to-Golgi pathway. Dominant negative mutants for these GTPases were co-expressed with fluorescent marker proteins as polyproteins separated by a 20 residue self-cleaving 2A peptide. Cleavage efficiency analysis of the generated polyproteins showed that functionality of the 2A peptide was influenced by several factors. This enabled us to design constructs with greatly increased cleavage efficiency compared to previous studies. The dominant negative GTPase variants resulting from cleavage of these 2A peptide constructs were found to be stable and active, and were successfully used to study the inhibitory effect on trafficking of the N-glycosylated CAH1 protein through the endomembrane system.

Conclusions/Significance: We demonstrate that the 2A peptide is a suitable tool when studying plant intracellular protein trafficking and that transient protoplast and in planta expression of mutant forms of SAR1 and RABD2a disrupts CAH1 trafficking. Similarly, expression of dominant ARF1 mutants also caused inhibition of CAH1 trafficking to a different extent. These results indicate that early trafficking of the plastid glycoprotein CAH1 depends on canonical vesicular transport mechanisms operating between the endoplasmic reticulum and Golgi apparatus.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-64040 (URN)10.1371/journal.pone.0051973 (DOI)000312386800122 ()
Available from: 2013-01-22 Created: 2013-01-14 Last updated: 2018-06-08Bibliographically approved
Baba, K., Karlberg, A., Schmidt, J., Schrader, J., Hvidsten, T., Bako, L. & Bhalerao, R. P. (2011). Activity-dormancy transition in the cambial meristem involves stage-specific modulation of auxin response in hybrid aspen.. Proceedings of the National Academy of Sciences of the United States of America, 108(8), 3418-23
Open this publication in new window or tab >>Activity-dormancy transition in the cambial meristem involves stage-specific modulation of auxin response in hybrid aspen.
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2011 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 108, no 8, p. 3418-23Article in journal (Refereed) Published
Abstract [en]

The molecular basis of short-day-induced growth cessation and dormancy in the meristems of perennial plants (e.g., forest trees growing in temperate and high-latitude regions) is poorly understood. Using global transcript profiling, we show distinct stage-specific alterations in auxin responsiveness of the transcriptome in the stem tissues during short-day-induced growth cessation and both the transition to and establishment of dormancy in the cambial meristem of hybrid aspen trees. This stage-specific modulation of auxin signaling appears to be controlled via distinct mechanisms. Whereas the induction of growth cessation in the cambium could involve induction of repressor auxin response factors (ARFs) and down-regulation of activator ARFs, dormancy is associated with perturbation of the activity of the SKP-Cullin-F-box(TIR) (SCF(TIR)) complex, leading to potential stabilization of repressor auxin (AUX)/indole-3-acetic acid (IAA) proteins. Although the role of hormones, such as abscisic acid (ABA) and gibberellic acid (GA), in growth cessation and dormancy is well established, our data now implicate auxin in this process. Importantly, in contrast to most developmental processes in which regulation by auxin involves changes in cellular auxin contents, day-length-regulated induction of cambial growth cessation and dormancy involves changes in auxin responses rather than auxin content.

Identifiers
urn:nbn:se:umu:diva-41060 (URN)10.1073/pnas.1011506108 (DOI)21289280 (PubMedID)
Available from: 2011-03-17 Created: 2011-03-17 Last updated: 2018-06-08Bibliographically approved
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