umu.sePublications
Change search
Link to record
Permanent link

Direct link
BETA
Hanson, Johannes
Publications (10 of 37) Show all publications
van der Horst, S., Snel, B., Hanson, J. & Smeekens, S. (2019). Novel pipeline identifies new upstream ORFs and non-AUG initiating main ORFs with conserved amino acid sequences in the 5 ' leader of mRNAs in Arabidopsis thaliana. RNA: A publication of the RNA Society, 25(3), 292-304
Open this publication in new window or tab >>Novel pipeline identifies new upstream ORFs and non-AUG initiating main ORFs with conserved amino acid sequences in the 5 ' leader of mRNAs in Arabidopsis thaliana
2019 (English)In: RNA: A publication of the RNA Society, ISSN 1355-8382, E-ISSN 1469-9001, Vol. 25, no 3, p. 292-304Article in journal (Refereed) Published
Abstract [en]

Eukaryotic mRNAs contain a 5' leader sequence preceding the main open reading frame (mORF) and, depending on the species, 20%-50% of eukaryotic mRNAs harbor an upstream ORF (uORF) in the 5' leader. An unknown fraction of these uORFs encode sequence conserved peptides (conserved peptide uORFs, CPuORFs). Experimentally validated CPuORFs demonstrated to regulate the translation of downstream mORFs often do so in a metabolite concentration-dependent manner. Previous research has shown that most CPuORFs possess a start codon context suboptimal for translation initiation, which turns out to be favorable for translational regulation. The suboptimal initiation context may even include non-AUG start codons, which makes CPuORFs hard to predict. For this reason, we developed a novel pipeline to identify CPuORFs unbiased of start codon using well-annotated sequence data from 31 eudicot plant species and rice. Our new pipeline was able to identify 29 novel Arabidopsis thaliana (Arabidopsis) CPuORFs, conserved across a wide variety of eudicot species of which 15 do not initiate with an AUG start codon. In addition to CPuORFs, the pipeline was able to find 14 conserved coding regions directly upstream and in frame with the mORF, which likely initiate translation on a non-AUG start codon. Altogether, our pipeline identified highly conserved coding regions in the 5' leaders of Arabidopsis transcripts, including in genes with proven functional importance such as LHY, a key regulator of the circadian clock, and the RAPTOR1 subunit of the target of rapamycin (TOR) kinase.

Place, publisher, year, edition, pages
Cold Spring Harbor Laboratory Press (CSHL), 2019
Keywords
5 '-UTR, translation, translational initiation, translational stalling, uORF
National Category
Biochemistry and Molecular Biology Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:umu:diva-157198 (URN)10.1261/rna.067983.118 (DOI)000459007300003 ()30567971 (PubMedID)
Projects
Bio4Energy
Available from: 2019-04-09 Created: 2019-04-09 Last updated: 2019-08-30Bibliographically approved
Bai, B., Novák, O., Ljung, K., Hanson, J. & Bentsink, L. (2018). Combined transcriptome and translatome analyses reveal a role for tryptophan-dependent auxin biosynthesis in the control of DOG1-dependent seed dormancy. New Phytologist, 217(3), 1077-1085
Open this publication in new window or tab >>Combined transcriptome and translatome analyses reveal a role for tryptophan-dependent auxin biosynthesis in the control of DOG1-dependent seed dormancy
Show others...
2018 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 217, no 3, p. 1077-1085Article in journal (Refereed) Published
Abstract [en]

The importance of translational regulation during Arabidopsis seed germination has been shown previously. Here the role of transcriptional and translational regulation during seed imbibition of the very dormant DELAY OF GERMINATION 1 (DOG1) near-isogenic line was investigated. Polysome profiling was performed on dormant and after-ripened seeds imbibed for 6 and 24 h in water and in the transcription inhibitor cordycepin. Transcriptome and translatome changes were investigated. Ribosomal profiles of after-ripened seeds imbibed in cordycepin mimic those of dormant seeds. The polysome occupancy of mRNA species is not affected by germination inhibition, either as a result of seed dormancy or as a result of cordycepin treatment, indicating the importance of the regulation of transcript abundance. The expression of auxin metabolism genes is discriminative during the imbibition of after-ripened and dormant seeds, which is confirmed by altered concentrations of indole-3-acetic acid conjugates and precursors.

Place, publisher, year, edition, pages
WILEY, 2018
Keywords
Arabidopsis thaliana, auxin, polysome profiling, ribosome, seed dormancy, seed germination, anscription
National Category
Botany Microbiology
Identifiers
urn:nbn:se:umu:diva-145161 (URN)10.1111/nph.14885 (DOI)000424541600015 ()29139127 (PubMedID)
Projects
Bio4Energy
Available from: 2018-02-26 Created: 2018-02-26 Last updated: 2019-08-30Bibliographically approved
Dubreuil, C., Jin, X., Barajas-López, J. d., Hewitt, T. C., Tanz, S. K., Dobrenel, T., . . . Strand, Å. (2018). Establishment of Photosynthesis through Chloroplast Development Is Controlled by Two Distinct Regulatory Phases. Plant Physiology, 176(2), 1199-1214
Open this publication in new window or tab >>Establishment of Photosynthesis through Chloroplast Development Is Controlled by Two Distinct Regulatory Phases
Show others...
2018 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 176, no 2, p. 1199-1214Article in journal (Refereed) Published
Abstract [en]

Chloroplasts develop from undifferentiated proplastids present in meristematic tissue. Thus, chloroplast biogenesis is closely connected to leaf development, which restricts our ability to study the process of chloroplast biogenesis per se. As a consequence, we know relatively little about the regulatory mechanisms behind the establishment of the photosynthetic reactions and how the activities of the two genomes involved are coordinated during chloroplast development. We developed a single cell-based experimental system from Arabidopsis (Arabidopsis thaliana) with high temporal resolution allowing for investigations of the transition from proplastids to functional chloroplasts. Using this unique cell line, we could show that the establishment of photosynthesis is dependent on a regulatory mechanism involving two distinct phases. The first phase is triggered by rapid light-induced changes in gene expression and the metabolome. The second phase is dependent on the activation of the chloroplast and generates massive changes in the nuclear gene expression required for the transition to photosynthetically functional chloroplasts. The second phase also is associated with a spatial transition of the chloroplasts from clusters around the nucleus to the final position at the cell cortex. Thus, the establishment of photosynthesis is a two-phase process with a clear checkpoint associated with the second regulatory phase allowing coordination of the activities of the nuclear and plastid genomes.

Place, publisher, year, edition, pages
American Society of Plant Biologists, 2018
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-140157 (URN)10.1104/pp.17.00435 (DOI)000424285500021 ()28626007 (PubMedID)
Projects
Bio4Energy
Available from: 2017-10-02 Created: 2017-10-02 Last updated: 2019-08-30Bibliographically approved
Yazdanpanah, F., Hanson, J., Hilhorst, H. W. M. & Bentsink, L. (2017). Differentially expressed genes during the imbibition of dormant and after-ripened seeds: a reverse genetics approach. BMC Plant Biology, 17(1), Article ID 151.
Open this publication in new window or tab >>Differentially expressed genes during the imbibition of dormant and after-ripened seeds: a reverse genetics approach
2017 (English)In: BMC Plant Biology, ISSN 1471-2229, E-ISSN 1471-2229, Vol. 17, no 1, article id 151Article in journal (Refereed) Published
Abstract [en]

BACKGROUND: Seed dormancy, defined as the incapability of a viable seed to germinate under favourable conditions, is an important trait in nature and agriculture. Despite extensive research on dormancy and germination, many questions about the molecular mechanisms controlling these traits remain unanswered, likely due to its genetic complexity and the large environmental effects which are characteristic of these quantitative traits. To boost research towards revealing mechanisms in the control of seed dormancy and germination we depend on the identification of genes controlling those traits.

METHODS: We used transcriptome analysis combined with a reverse genetics approach to identify genes that are prominent for dormancy maintenance and germination in imbibed seeds of Arabidopsis thaliana. Comparative transcriptomics analysis was employed on freshly harvested (dormant) and after-ripened (AR; non-dormant) 24-h imbibed seeds of four different DELAY OF GERMINATION near isogenic lines (DOGNILs) and the Landsberg erecta (Ler) wild type with varying levels of primary dormancy. T-DNA knock-out lines of the identified genes were phenotypically investigated for their effect on dormancy and AR.

RESULTS: We identified conserved sets of 46 and 25 genes which displayed higher expression in seeds of all dormant and all after-ripened DOGNILs and Ler, respectively. Knock-out mutants in these genes showed dormancy and germination related phenotypes.

CONCLUSIONS: Most of the identified genes had not been implicated in seed dormancy or germination. This research will be useful to further decipher the molecular mechanisms by which these important ecological and commercial traits are regulated.

Keywords
Arabidopsis thaliana, Delay of germination, Knockout lines, Seed performance, Transcriptromics
National Category
Botany Developmental Biology
Identifiers
urn:nbn:se:umu:diva-140148 (URN)10.1186/s12870-017-1098-z (DOI)000410946400001 ()28893189 (PubMedID)
Projects
Bio4Energy
Available from: 2017-10-02 Created: 2017-10-02 Last updated: 2019-08-30Bibliographically approved
Ferrando, A., Mar Castellano, M., Lison, P., Leister, D., Stepanova, A. N. & Hanson, J. (2017). Editorial: Relevance of Translational Regulation on Plant Growth and Environmental Responses. Frontiers in Plant Science, 8, Article ID 2170.
Open this publication in new window or tab >>Editorial: Relevance of Translational Regulation on Plant Growth and Environmental Responses
Show others...
2017 (English)In: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 8, article id 2170Article in journal, Editorial material (Other academic) Published
Place, publisher, year, edition, pages
Frontiers Media S.A., 2017
Keywords
mRNA translation, translation factors, post-transcriptional regulation, translatome, organellar gene expression
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-143641 (URN)10.3389/fpls.2017.02170 (DOI)000418251100001 ()
Available from: 2018-01-08 Created: 2018-01-08 Last updated: 2018-06-09Bibliographically approved
Bai, B., Peviani, A., van der Horst, S., Gamm, M., Snel, B., Bentsink, L. & Hanson, J. (2017). Extensive translational regulation during seed germination revealed by polysomal profiling. New Phytologist, 214(1), 233-244
Open this publication in new window or tab >>Extensive translational regulation during seed germination revealed by polysomal profiling
Show others...
2017 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 214, no 1, p. 233-244Article in journal (Refereed) Published
Abstract [en]

This work investigates the extent of translational regulation during seed germination. The polysome occupancy of each gene is determined by genome-wide profiling of total mRNA and polysome-associated mRNA. This reveals extensive translational regulation during Arabidopsis thaliana seed germination. The polysome occupancy of thousands of individual mRNAs changes to a large extent during the germination process. Intriguingly, these changes are restricted to two temporal phases (shifts) during germination, seed hydration and germination. Sequence features, such as upstream open reading frame number, transcript length, mRNA stability, secondary structures, and the presence and location of specific motifs correlated with this translational regulation. These features differed significantly between the two shifts, indicating that independent mechanisms regulate translation during seed germination. This study reveals substantial translational dynamics during seed germination and identifies development-dependent sequence features and cis elements that correlate with the translation control, uncovering a novel and important layer of gene regulation during seed germination.

Keywords
Arabidopsis, germination, imbibition, polysomal profiling, ribosome, RNA structure, seedling establishment, translatomics
National Category
Botany
Research subject
biology; Physiological Botany
Identifiers
urn:nbn:se:umu:diva-132004 (URN)10.1111/nph.14355 (DOI)000398130300023 ()27935038 (PubMedID)
Projects
Bio4Energy
Available from: 2017-03-01 Created: 2017-03-01 Last updated: 2019-08-30Bibliographically approved
Baena-González, E. & Hanson, J. (2017). Shaping plant development through the SnRK1–TOR metabolic regulators [Letter to the editor]. Current opinion in plant biology, 35, 152-157
Open this publication in new window or tab >>Shaping plant development through the SnRK1–TOR metabolic regulators
2017 (English)In: Current opinion in plant biology, ISSN 1369-5266, E-ISSN 1879-0356, Vol. 35, p. 152-157Article in journal, Letter (Refereed) Published
Abstract [en]

SnRK1 (Snf1-related protein kinase 1) and TOR (target of rapamycin) are evolutionarily conserved protein kinases that lie at the heart of energy sensing, playing central and antagonistic roles in the regulation of metabolism and gene expression. Increasing evidence links these metabolic regulators to numerous aspects of plant development, from germination to flowering and senescence. This prompts the hypothesis that SnRK1 and TOR modify developmental programs according to the metabolic status to adjust plant growth to a specific environment. The aim of this review is to provide support to this hypothesis and to incentivize further studies on this topic by summarizing the work that establishes a genetic connection between SnRK1-TOR and plant development.

National Category
Botany
Identifiers
urn:nbn:se:umu:diva-132002 (URN)10.1016/j.pbi.2016.12.004 (DOI)000396959300023 ()28027512 (PubMedID)
Projects
Bio4Energy
Available from: 2017-03-01 Created: 2017-03-01 Last updated: 2019-08-30Bibliographically approved
Weiste, C., Pedrotti, L., Selvanayagam, J., Muralidhara, P., Fröschel, C., Novák, O., . . . Dröge-Laser, W. (2017). The Arabidopsis bZIP11 transcription factor links low-energy signalling to auxin-mediated control of primary root growth. PLoS Genetics, 13(2)
Open this publication in new window or tab >>The Arabidopsis bZIP11 transcription factor links low-energy signalling to auxin-mediated control of primary root growth
Show others...
2017 (English)In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 13, no 2Article in journal (Refereed) Published
Abstract [en]

Plants have to tightly control their energy homeostasis to ensure survival and fitness under constantly changing environmental conditions. Thus, it is stringently required that energy-consuming stress-adaptation and growth-related processes are dynamically tuned according to the prevailing energy availability. The evolutionary conserved SUCROSE NON-FERMENTING1 RELATED KINASES1 (SnRK1) and the downstream group C/S1 basic leucine zipper (bZIP) transcription factors (TFs) are well-characterised central players in plants' low-energy management. Nevertheless, mechanistic insights into plant growth control under energy deprived conditions remains largely elusive. In this work, we disclose the novel function of the low-energy activated group S1 bZIP11-related TFs as regulators of auxin-mediated primary root growth. Whereas transgenic gain-of-function approaches of these bZIPs interfere with the activity of the root apical meristem and result in root growth repression, root growth of loss-of-function plants show a pronounced insensitivity to low-energy conditions. Based on ensuing molecular and biochemical analyses, we propose a mechanistic model, in which bZIP11-related TFs gain control over the root meristem by directly activating IAA3/SHY2 transcription. IAA3/SHY2 is a pivotal negative regulator of root growth, which has been demonstrated to efficiently repress transcription of major auxin transport facilitators of the PIN-FORMED (PIN) gene family, thereby restricting polar auxin transport to the root tip and in consequence auxin-driven primary root growth. Taken together, our results disclose the central low-energy activated SnRK1-C/S1-bZIP signalling module as gateway to integrate information on the plant's energy status into root meristem control, thereby balancing plant growth and cellular energy resources.

National Category
Botany Genetics
Identifiers
urn:nbn:se:umu:diva-132003 (URN)10.1371/journal.pgen.1006607 (DOI)000395719300024 ()28158182 (PubMedID)
Projects
Bio4Energy
Available from: 2017-03-01 Created: 2017-03-01 Last updated: 2019-08-30Bibliographically approved
He, H., Willems, L., Batushansky, A., Fait, A., Hanson, J., Nijveen, H., . . . Bentsink, L. (2016). Effects of Parental Temperature and Nitrate on Seed Performance are Reflected by Partly Overlapping Genetic and Metabolic Pathways. Plant and Cell Physiology, 57(3), 473-487
Open this publication in new window or tab >>Effects of Parental Temperature and Nitrate on Seed Performance are Reflected by Partly Overlapping Genetic and Metabolic Pathways
Show others...
2016 (English)In: Plant and Cell Physiology, ISSN 0032-0781, E-ISSN 1471-9053, Vol. 57, no 3, p. 473-487Article in journal (Refereed) Published
Abstract [en]

Seed performance is affected by the seed maturation environment and previously, we have shown that temperature, nitrate and light intensity were the most influential environmental factors affecting seed performance. Seeds developed in these environments were selected to assess the underlying metabolic pathways, using a combination of transcriptomics and metabolomics. These analyses revealed that the effects of the temperature and nitrate parental environments were reflected by partly overlapping genetic and metabolic networks, as indicated by similar changes in metabolites and transcripts expression levels. Nitrogen-metabolism related metabolites (asparagine, GABA and allantoin) were significantly decreased in both low temperature (15°C) and low nitrate (N0) maturation environments. Correspondingly, nitrogen-metabolism genes (ALLANTOINASE, NITRATE REDUCTASE 1, NITRITE REDUCTASE 1 and NITRILASE 4) were differentially regulated in the low temperature and nitrate maturation environments, as compared with control conditions. High light intensity during seed maturation increased galactinol content, and displayed a high correlation with seed longevity. Low light had a genotype-specific effect on cell surface encoding genes in the DELAY OF GERMINATION 6-Near Isogenic Line (NILDOG6). Overall, the integration of phenotypes, metabolites and transcripts led to new insights in the regulation of seed performance.

Place, publisher, year, edition, pages
Oxford University Press, 2016
Keywords
Light intensity, Metabolites, Nitrate, Seed maturation, Temperature, Transcriptome
National Category
Cell Biology
Identifiers
urn:nbn:se:umu:diva-114428 (URN)10.1093/pcp/pcv207 (DOI)000374572400004 ()26738545 (PubMedID)
Projects
Bio4Energy
Available from: 2016-01-18 Created: 2016-01-18 Last updated: 2019-08-30Bibliographically approved
Nukarinen, E., Nägele, T., Pedrotti, L., Wurzinger, B., Mair, A., Landgraf, R., . . . Weckwerth, W. (2016). Quantitative phosphoproteomics reveals the role of the AMPK plant ortholog SnRK1 as a metabolic master regulator under energy deprivation. Scientific Reports, 6, Article ID 31697.
Open this publication in new window or tab >>Quantitative phosphoproteomics reveals the role of the AMPK plant ortholog SnRK1 as a metabolic master regulator under energy deprivation
Show others...
2016 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 31697Article in journal (Refereed) Published
Abstract [en]

Since years, research on SnRK1, the major cellular energy sensor in plants, has tried to define its role in energy signalling. However, these attempts were notoriously hampered by the lethality of a complete knockout of SnRK1. Therefore, we generated an inducible amiRNA::SnRK1α2 in a snrk1α1 knock out background (snrk1α1/α2) to abolish SnRK1 activity to understand major systemic functions of SnRK1 signalling under energy deprivation triggered by extended night treatment. We analysed the in vivo phosphoproteome, proteome and metabolome and found that activation of SnRK1 is essential for repression of high energy demanding cell processes such as protein synthesis. The most abundant effect was the constitutively high phosphorylation of ribosomal protein S6 (RPS6) in the snrk1α1/α2 mutant. RPS6 is a major target of TOR signalling and its phosphorylation correlates with translation. Further evidence for an antagonistic SnRK1 and TOR crosstalk comparable to the animal system was demonstrated by the in vivo interaction of SnRK1α1 and RAPTOR1B in the cytosol and by phosphorylation of RAPTOR1B by SnRK1α1 in kinase assays. Moreover, changed levels of phosphorylation states of several chloroplastic proteins in the snrk1α1/α2 mutant indicated an unexpected link to regulation of photosynthesis, the main energy source in plants.

Place, publisher, year, edition, pages
Nature Publishing Group, 2016
National Category
Cell Biology
Identifiers
urn:nbn:se:umu:diva-125540 (URN)10.1038/srep31697 (DOI)000381706800001 ()27545962 (PubMedID)
Projects
Bio4Energy
Available from: 2016-09-19 Created: 2016-09-13 Last updated: 2019-08-30Bibliographically approved
Organisations

Search in DiVA

Show all publications