Richard G H Immink

Richard G H Immink
Wageningen University & Research | WUR · Faculty of Plant Sciences

Prof. dr. ir.

About

194
Publications
37,377
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6,807
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Additional affiliations
January 2007 - December 2012
Wageningen University & Research
January 2004 - December 2012

Publications

Publications (194)
Article
Full-text available
The MADS transcription factors (TF) are an ancient eukaryotic protein family. In plants, the family is divided into two main lineages. Here, we demonstrate that DNA binding in both lineages absolutely requires a short amino acid sequence C-terminal to the MADS domain (M domain) called the Intervening domain (I domain) that was previously defined on...
Article
Full-text available
Key message Understanding the molecular network, including protein-protein interactions, of VRS5 provide new routes towards the identification of other key regulators of plant architecture in barley. Abstract The TCP transcriptional regulator TEOSINTE BRANCHED 1 (TB1) is a key regulator of plant architecture. In barley, an important cereal crop, H...
Article
Full-text available
Key message Comprehensive analysis of the FT/TFL1 gene family in Passiflora organensis results in understanding how these genes might be involved in the regulation of the typical plant architecture presented by Passiflora species. Passion fruit (Passiflora spp) is an economic tropical fruit crop, but there is hardly any knowledge available about th...
Article
Full-text available
Certain obligate parasites induce complex and substantial phenotypic changes in their hosts in ways that favor their transmission to other trophic levels. However, the mechanisms underlying these changes remain largely unknown. Here we demonstrate how SAP05 protein effectors from insect-vectored plant pathogenic phytoplasmas take control of several...
Article
Full-text available
The MADS transcription factors (TF) are an ancient eukaryotic protein family. In plants, the family is divided into two main lineages. Here, we demonstrate that DNA binding in both lineages absolutely requires a short amino acid sequence C-terminal to the MADS domain (M domain) called the Intervening domain (I domain) that was previously defined on...
Article
Full-text available
HEAT SHOCK FACTOR A2 (HSFA2) is a regulator of multiple environmental stress responses required for stress acclimation. We analyzed HSFA2 co-regulated genes and identified 43 genes strongly co-regulated with HSFA2 during multiple stresses. Motif enrichment analysis revealed an over-representation of the site II element (SIIE) in the promoters of th...
Preprint
Full-text available
Barley is the fourth largest cereal crop grown worldwide, and essential for food and feed production. Phenotypically, the barley spike, which is unbranched, occurs in two main architectural shapes: two-rowed or six-rowed. In the 6-rowed cultivars, all three florets of the triple floret meristem develop into seeds while in 2-rowed lines only the cen...
Preprint
The MADS transcription factors (TF) are an ancient protein family with a high degree of sequence identity that bind almost identical DNA sequences across all eukaryotic kingdoms of life, yet fulfill dramatically different physiological roles. In plants, the family is divided into two main lineages, type I and II, based on sequence conservation of t...
Preprint
Full-text available
The MADS transcription factors (TF) are an ancient protein family with a high degree of sequence identity that bind almost identical DNA sequences across all eukaryotic kingdoms of life, yet fulfill dramatically different physiological roles. In plants, the family is divided into two main lineages, type I and II, based on sequence conservation of t...
Article
Full-text available
Geophytes, the plants that form vegetative storage organs, are characterized by a dual reproduction system, in which vegetative and sexual propagation are tightly regulated to ensure fitness in harsh climatic conditions. Recent findings highlight the role of the PEBP (PHOSPHATIDYLETHANOLAMINE-BINDING PROTEINS) gene family in geophytes as major play...
Preprint
Full-text available
Obligate parasites can induce complex and substantial phenotypic changes in their hosts in ways that favour their transmission to other trophic levels. However, mechanisms underlying these changes remain largely unknown. Here, we demonstrate how SAP05 protein effectors from insect-vectored plant pathogenic phytoplasmas take control of several plant...
Preprint
Full-text available
The control of branch outgrowth is critical for plant fitness, stress resilience and crop yield. The Arabidopsis thaliana transcription factor BRANCHED1 (BRC1) plays a pivotal role in this process as it integrates signals that inhibit axillary bud growth to control shoot branching. Despite the remarkable activity of BRC1 as a potent growth inhibito...
Preprint
Full-text available
Phytoplasmas are pathogenic bacteria that reprogram plant host development in order to attract their insect vectors to disseminate. Previous studies have characterized a few different phytoplasma effector proteins that supress specific transcription factors. However, these are only a small fraction of the potential effectors used by phytoplasmas, m...
Article
Full-text available
Members of the Arabidopsis thaliana TCP transcription factor (TF) family affect plant growth and development. We systematically quantified the effect of mutagenizing single or multiple TCP TFs and how altered vegetative growth or branching influences final seed yield. We monitored rosette growth over time and branching patterns and seed yield chara...
Article
Motivation: Predicting residue-residue contacts between interacting proteins is an important problem in bioinformatics. The growing wealth of sequence data can be used to infer these contacts through correlated mutation analysis on multiple sequence alignments of interacting homologs of the proteins of interest. This requires correct identificatio...
Article
Full-text available
Background: Long non-coding RNAs (lncRNAs) have emerged as new class of regulatory molecules in animals where they regulate gene expression at transcriptional and post-transcriptional level. Recent studies also identified lncRNAs in plant genomes, revealing a new level of transcriptional complexity in plants. Thousands of lncRNAs have been predict...
Article
Full-text available
Key message: Tulip vegetative reproduction. Tulips reproduce asexually by the outgrowth of their axillary meristems located in the axil of each bulb scale. The number of axillary meristems in one bulb is low, and not all of them grow out during the yearly growth cycle of the bulb. Since the degree of axillary bud outgrowth in tulip determines the...
Data
Figure S2. Construction, expression and leaf phenotype of ATML1 pro :TCP5‐GFP.
Data
Figure S3. Floral phenotypes in TCP5 overexpression and mutant lines.
Data
Table S3. List of Gene Ontology terms (full analysis).
Data
Figure S1. Expression pattern of TCP5 in Arabidopsis petals during early and later stages of flower development.
Data
Figure S7. Phenotypes of the 35S pro :TCP5‐GR mutant after dexamethasone treatment.
Data
Figure S8. Phenotypical alterations in petals of mutants deficient in ethylene reception and signal transduction.
Data
Table S1. Lists of differentially expressed genes after RNA‐seq analysis of all samples used in this study.
Data
Figure S4. Graphic representation accompanying the cell morphology phenotyping.
Article
Full-text available
During the plant life cycle, diverse signalling inputs are continuously integrated and engage specific genetic programs depending on the cellular or developmental context. Consistent with an important role in this process, HECATE (HEC) bHLH transcription factors display diverse functions, from photomorphogenesis to the control of shoot meristem dyn...
Article
Flowers of most dicotyledons have petals that, together with the sepals, initially protect the reproductive organs. Later during development petals are required to open the flower and to attract pollinators. These diverse set of functions demand a tight temporal and spatial regulation of petal development. We studied the functioning of the Arabidop...
Preprint
Full-text available
During the plant life cycle, diverse signalling inputs are continuously integrated and engage specific genetic programs depending on the cellular or developmental context. Consistent with an important role in this process, HECATE (HEC) bHLH transcription factors display diverse functions, from photomorphogenesis to the control of shoot meristem dyn...
Preprint
Full-text available
Predicting residue-residue contacts between interacting proteins is an important problem in bioinformatics. The growing wealth of sequence data can be used to infer these contacts through correlated mutation analysis on multiple sequence alignments of interacting homologs of the proteins of interest. This requires correct identification of pairs of...
Article
Full-text available
Background The chromosome conformation capture (3C) technique is a method to study chromatin interactions at specific genomic loci. Initially established for yeast the 3C technique has been adapted to plants in recent years in order to study chromatin interactions and their role in transcriptional gene regulation. As the plant scientific community...
Article
Full-text available
Floral induction in Tulipa gesneriana and Lilium longiflorum is triggered by contrasting temperature conditions, high and low temperature respectively. In Arabidopsis, the floral integrator FLOWERING LOCUS T (FT), member of the PEBP gene family, is a key player in flowering time control. In this study, one PEBP gene was identified and characterized...
Article
Full-text available
Background: Floral timing is a carefully regulated process, in which the plant determines the optimal moment to switch from the vegetative to reproductive phase. While there are numerous genes known that control flowering time, little information is available on chemical compounds that are able to influence this process. We aimed to discover novel...
Article
Full-text available
Background Global warming severely affects flowering time and reproductive success of plants. Alternative splicing of pre-messenger RNA (mRNA) is an important mechanism underlying ambient temperature-controlled responses in plants, yet its regulation is poorly understood. An increase in temperature promotes changes in plant morphology as well as th...
Article
Full-text available
Plants adjust their development and architecture to small variations in ambient temperature. In a time in which temperatures are rising world-wide, the mechanism by which plants are able to sense temperature fluctuations and adapt to it, is becoming of special interest. By performing RNA-sequencing on two Arabidopsis accession and one Brassica spec...
Data
Validation of RNAseq results by qPCR (DOCX)
Data
Flowering time analysis of A. thaliana Gy-0. (DOCX)
Data
Overview of all differential splicing events in this study, reciprocally spliced genes, genes in BiNGO analysis, spliced splicing genes. (XLSX)
Data
Sequence alignment of MAF3 isoforms (DOCX)
Data
Oligo’s used in this study. (DOCX)
Data
Detected splicing event counts. (DOCX)
Data
Alignments of all differential events A. thaliana Col-0 low temperature. (PDF)
Data
Alignments of all differential events B. oleracea. (PDF)
Data
Alignments of all differential events A. thaliana Col-0 high temperature. (PDF)
Data
Alignments of all differential events A. thaliana Gy-0. (PDF)
Article
Shoot-branching patterns determine key aspects of plant life and are important targets for crop breeding. However, we are still largely ignorant of the genetic networks controlling locally the most important decision during branch development: whether the axillary bud, or branch primordium, grows out to give a lateral shoot or remains dormant. Here...