Julia Kehr

University of Hamburg | UHH · Biocenter Klein Flottbek and Botanical Garden (BioZ Flottbek)

Ribosome biogenesis is a key process in all eukaryotic cells that requires hundreds of ribosome biogenesis factors (RBFs), which are essential to build the mature ribosomes consisting of proteins and rRNAs. The processing of the required rRNAs has been studied extensively in yeast and mammals, but in plants much is still unknown. In this study, we...

The long-distance transport of messenger RNAs (mRNAs) has been shown to be important for several developmental processes in plants. A popular method for identifying travelling mRNAs is to perform RNA-Seq on grafted plants. This approach depends on the ability to correctly assign sequenced mRNAs to the genetic background from which they originated....

The HSC70/HSP70 family of heat shock proteins are evolutionarily conserved chaperones involved in protein folding, protein transport, and RNA binding. Arabidopsis HSC70 chaperones are thought to act as housekeeping chaperones and as such are involved in many growth‐related pathways. Whether Arabidopsis HSC70 binds RNA and whether this interaction i...

In higher plants, long-distance RNA transport via the phloem is crucial for communication between distant plant tissues to align development with stress responses and reproduction. Several recent studies suggest that specific RNAs are among the potential long-distance information transmitters. However, it is yet not well understood how these RNAs e...

There is now a wealth of data, from different plants and labs and spanning more than two decades, which unequivocally demonstrates that RNAs can be transported over long distances, from the cell where they are transcribed to distal cells in other tissues. Different types of RNA molecules are transported, including micro- and messenger RNAs. Whether...

Heat shock proteins of the HSC70/HSP70 family are evolutionarily conserved chaperones that are involved in protein folding, protein transport and RNA binding. Arabidopsis HSC70 chaperones are thought to act as housekeeping chaperones and as such are involved in many growth-related pathways. Whether Arabidopsis HSC70 binds RNA and its function has r...

Northern blotting is a classical technique that allows the detection of specific nucleic acids using radioactive or non-radioactive probes. Normally, nucleic acids are denatured and separated by agarose or polyacrylamide gel electrophoresis and transferred and fixed to a membrane prior to detection. Here, we describe a method to analyze specific RN...

Cyclophilins (CYPs) are a group of ubiquitous prolyl cis/trans isomerases (PPIases). It was shown that plants possess the most diverse CYP families and that these are abundant in the phloem long-distance translocation stream. Since phloem exudate showed PPIase activity, three single-domain CYPs that occur in phloem samples from Brassica napus were...

Salinity stress is a major abiotic stress that affects plant growth and limits crop production. Roots are the primary site of salinity perception, and salt sensitivity in roots limits the productivity of the entire plant. To better understand salt stress responses in canola, we performed a comparative proteomic analysis of roots from the salt-toler...

Contents Summary 29 I. Introduction 29 II. Phloem as a conduit for macromolecules 30 III. Classes of phloem transported RNAs and their function 32 IV. Mode of RNA transport 35 V. Conclusions 37 Acknowledgements 37 References 37 Summary In higher plants, small noncoding RNA s and large messenger RNA ( mRNA ) molecules are transported betwee...

Sampling the phloem of higher plants is often laborious and significantly dependent on the plant species. However, proteome studies under denaturing conditions could be achieved in different plant species. Native protein:protein and protein:nucleic acid complexes from phloem samples have as yet scarcely been analyzed, although they might play impor...

Plants face different nutrient limitations during their lifecycles that can occur in agriculturally used soils, as well as in natural habitats. Growth, reproduction, and yield are often limited by the essential macronutrients phosphorus, nitrogen, potassium, calcium, magnesium, and sulfur. Due to the sessile nature of plants, it is essential for th...

RNA-seq processing, number of cDNA sequence reads obtained for bacterial community of C. saccharophila (MZCH 10155), S. quadricauda (MZCH 10104), and M. crux-melitensis (MZCH 98). The results represent the average value of 3 replicas.

Transcriptomic assignment of the first most abundant 1000 hits of the S. quadricauda (MZCH 10104) RNA seq dataset including functions and pathways.

Overview transcriptomic assignment including function, COGs and counting of the RNA seq data of C. saccharophila (MZCH 10155), S. quadricauda (MZCH 10104), and M. crux-melitensis (MZCH 98), minimum RPKM value: 10.0.

Transcriptomic assignment of the first most abundant 1000 hits of the M. crux-melitensis (MZCH 98) including functions and pathways.

List of proteins observed in the common elements of LC/MS-MS analysis of S. quadricauda (MZCH 10104) including the overlap between secretome and transcriptome datasets and phylogenetic assignment.

Overall number of contigs generated for bacterial community of C. saccharophila (MZCH 10155), Scenedesmus quadricauda (MZCH 10104) and Micrasterias crux-melitensis (MZCH 98), including protein coding genes and data source.

Bin overview of the bacterial community of C. saccharophila (MZCH 10155), S. quadricauda (MZCH 10104), and M. crux-melitensis (MZCH 98) including phylogenetic assignment (consensus score > 0.8), completeness (mainly mine cut off 70.0%, *low quality bins 25.2-66.4%), genome size and GC content.

Transcriptomic assignment of the first most abundant 1000 hits of the C. saccharophila (MZCH 10155) RNA seq dataset including functions and pathways.

Microalga are of high relevance for the global carbon cycling and it is well-known that they are associated with a microbiota. However, it remains unclear, if the associated microbiota, often found in phycosphere biofilms, is specific for the microalga strains and which role individual bacterial taxa play. Here we provide experimental evidence that...

Cyclophilins (CYPs) are a group of ubiquitous proteins characterized by their ability to bind to the immunosuppressive drug cyclosporin A. The CYP family occurs in a wide range of organisms and contains a conserved peptidyl-prolyl cis/trans isomerase domain. In addition to fulfilling a basic role in protein folding, CYPs may also play diverse impor...

Fig. S1 Overview of a 2D gel electrophoresis approach for the identification of protein complexes in oilseed rape phloem sap. Table S1 Oligonucleotides used to detect rRNAs in the phloem sap of Brassica napus Table S2 List of proteins identified by MALDI‐TOF MS from complex I corresponding to the spot numbers in Fig. 2(a) Table S3 List of protei...

Phloem sap contains a large number of macromolecules, including proteins and RNAs from different classes. Proteome analyses of phloem samples from different plant species under denaturing conditions identified hundreds of proteins potentially involved in diverse processes. Surprisingly, these studies also found a significant number of ribosomal and...

Background: Grafting is a well-established technique for studying long-distance transport and signalling processes in higher plants. While oilseed rape has been the subject of comprehensive analyses of xylem and phloem sap to identify macromolecules potentially involved in long-distance information transfer, there is currently no standardised graf...

Cucurbits developed the unique extrafascicular phloem (EFP) as a defensive structure against herbivorous animals. Mechanical leaf injury was previously shown to induce a systemic wound response in the EFP of pumpkin (Cucurbita maxima). Here, we demonstrate that the phloem antioxidant system and protein modifications by NO are strongly regulated dur...

The aim of this work was to study the effect of Fe deficiency on the protein profile of phloem sap exudates from Brassica napus using 2-DE (IEF-SDS PAGE). The experiment was repeated thrice and two technical replicates per treatment were done. Phloem sap purity was assessed by measuring sugar concentrations. Two hundred sixty-three spots were consi...

The presented invention relates to the field of agriculture and of energy (biofuel) production. In particular it relates to plants that have been modified to be cropped and used as source of fermentable sugars.

Protein profiles of inner (IE) and outer (OE) chloroplast envelope membrane preparations from pea were studied using shotgun nLC-MS/MS and two-dimensional electrophoresis, and 589 protein species (NCBI entries) were identified. The relative enrichment of each protein in the IE/OE pair of membranes was used to provide an integrated picture of the ch...

The clubroot disease caused by the obligate biotrophic protist Plasmodiophora brassicae on host plants of the Brassicaceae family is characterized by enhanced cell division and cell expansion. Since a typical root section of an infected plant always includes different stages of the pathogen as well as uninfected cells, we were interested to investi...

The aim of this study was to obtain a comprehensive overview of the phloem sap protein profile of Lupinus texensis, with a special focus on proteins binding Fe and Zn. Lupinus texensis was chosen as model plant given the simplicity to obtain exudates from sieve elements. Protein profiling by 2-DE revealed 249 spots, and 54 of them were unambiguousl...

Plants frequently have to cope with environments with sub-optimal mineral nutrient availability. Therefore they need to constantly sense changes of ion concentrations in their environment. Nutrient availabilities and needs have to be tightly coordinated between organs to ensure a balance between uptake and demand for metabolism, growth, reproductio...

The transport tubes of the phloem are essential for higher plants. They not only provide the route for the distribution of assimilates produced during photosynthesis from source to sink organs but also (re-) distribute mineral nutrients. Additionally, the phloem is essential for sending information between distant plant organs and steering developm...

Many physiological processes are limited to specific tissues or even specific cell types. Analysing entire plants or organs results in averaged data of all cell types contained in the sample; thus, specific metabolic functions cannot be assigned to individual cell types. A higher spatial resolution is required. By microdissecting plant organs, homo...

The phloem is known as the main conduit for assimilates synthesized during photosynthesis, but also spreads signals coordinating important developmental decisions and physiological responses between plant organs. Among the wealth of potential signaling molecules, RNAs have outstanding potential, because they allow the transmission of sequence-speci...

This chapter provides an overview of experimental strategies that have been successfully employed to identify RNAs in sieve-tube sap and a summary of the different types of RNAs that have been identified. In addition, the methods to examine RNA mobility and potential physiological roles RNAs might play in the complex long-distance communication net...

In natural environments, plants frequently have to cope with insufficient nutrient supply, which significantly impairs crop yield. Nutrients have to be optimally distributed to permit the best possible growth and reproduction. To react to nutrient deficiencies, plants have evolved a broad spectrum of diverse metabolic, physiological and development...

The intricate assembly of photosystem I (PSI), a large multiprotein complex in the thylakoid membrane, depends on auxiliary protein factors. One of the essential assembly factors for PSI is encoded by ycf3 (hypothetical chloroplast reading frame number 3) in the chloroplast genome of algae and higher plants. To identify novel factors involved in PS...

Aphididae feed upon the plant sieve elements (SE), where they ingest sugars, nitrogen compounds and other nutrients. For ingestion, aphid stylets penetrate SE, and because of the high hydrostatic pressure in SE, phloem sap exudes out into the stylets. Severing stylets to sample phloem exudates (i.e. stylectomy) has been used extensively for the stu...

Comparison of sRNA abundances in phloem, leaves and roots. sRNA microarray comparison of phloem (blue), leaf (green) and root (red) tissue of Brassica napus plants from biologically independent replications (n = 3). To allow inter-array comparison, signal intensities were normalized to the median signal of each sample. Only known miRNAs present on...

Sequences of the unknown phloem sap sRNAs represented on the microarrays. Phloem sap small RNA sequences of Brassica napus (Bn_PsRNAs) that were contained on the sRNA microarray (sequences were derived from high-throughput sequencing of B. napus phloem sap published in [1]).

Comparison of miRNA abundance in phloem sap vs. inflorescence stem. Comparison of sRNA microarray analysis of stem tissue (green) and phloem sap (blue) of Brassica napus. Only known miRNAs present on the commercial array, only one member per family are depicted. The upper graphs show the signal intensities on the array while the lower depict the lo...

Transcript analysis of known nutrient stress-specific genes. Transcript analysis of known nutrient stress-specific genes in leaf and root tissue of hydroponically grown Brassica napus plants by semi-quantitative RT-PCR after 25, 30 and 35 cycles under -S, -Cu and -Fe compared to full nutrition (FN).

Accumulation of three miR395 targets in WT and hen1-1 shoots grown under full nutrition. Levels of the targets SULTR2;1, APS1 and APS4 in shoots as detected by sqRT-PCR (35 cycles, UBC10, At5g53300 served as a control). FN: full nutrition.

List of oligonucleotides used. Oligonucleotide sequences used for the detection of nutrient stress-specific miRNAs by RNA gel blots or by semi-quantitative RT-PCR, for the analysis of miR395 target genes, and for transcript detection of nutrient-responsive genes by semi-quantitative RT-PCR.

Nutrient availabilities and needs have to be tightly coordinated between organs to ensure a balance between uptake and consumption for metabolism, growth, and defense reactions. Since plants often have to grow in environments with sub-optimal nutrient availability, a fine tuning is vital. To achieve this, information has to flow cell-to-cell and ov...