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Publications - Molecular Signal Processing

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Schumann, N.; Navarro-Quezada, A.; Ullrich, K.; Kuhl, C.; Quint, M. Molecular Evolution and Selection Patterns of Plant F-box Proteins with C-terminal Kelch Repeats Plant Physiol 155, 835-850, (2011) DOI: 10.1104/pp.110.166579

The F-box protein superfamily represents one of the largest families in the plant kingdom. F-box proteins phylogenetically organize into numerous subfamilies characterized by their carboxyl (C)-terminal protein-protein interaction domain. Among the largest F-box protein subfamilies in plant genomes are those with C-terminal kelch repeats. In this study, we analyzed the phylogeny and evolution of F-box kelch proteins/genes (FBKs) in seven completely sequenced land plant genomes including a bryophyte, a lycophyte, monocots, and eudicots. While absent in prokaryotes, F-box kelch proteins are widespread in eukaryotes. Nonplant eukaryotes usually contain only a single FBK gene. In land plant genomes, however, FBKs expanded dramatically. Arabidopsis thaliana, for example, contains at least 103 F-box genes with well-conserved C-terminal kelch repeats. The construction of a phylogenetic tree based on the full-length amino acid sequences of the FBKs that we identified in the seven species enabled us to classify FBK genes into unstable/stable/superstable categories. In contrast to superstable genes, which are conserved across all seven species, kelch domains of unstable genes, which are defined as lineage specific, showed strong signatures of positive selection, indicating adaptational potential. We found evidence for conserved protein features such as binding affinities toward A. thaliana SKP1-like adaptor proteins and subcellular localization among closely related FBKs. Pseudogenization seems to occur only rarely, but differential transcriptional regulation of close relatives may result in subfunctionalization.

Bürstenbinder, K.; Savchenko, T.; Müller, J.; Adamson, A.W.; Stamm, G.; Kwong, R.; Zipp, B.J.; Dhurvas Chandrasekaran, D. & Abel, S. Arabidopsis calmodulin-binding protein IQ67-domain 1 localizes to microtubules and interacts with kinesin light chain-related protein-1 J Biol Chem 288, 1871-1882, (2013) DOI: 10.1074/jbc.M112.396200

Calcium (Ca2+) is a key second messenger in eukaryotes and regulates diverse cellular processes, most notably via calmodulin (CaM). In Arabidopsis thaliana, IQD1 (IQ67 domain 1) is the founding member of the IQD family of putative CaM targets. The 33 predicted IQD proteins share a conserved domain of 67 amino acids that is characterized by a unique arrangement of multiple CaM recruitment motifs, including so-called IQ motifs. Whereas IQD1 has been implicated in the regulation of defense metabolism, the biochemical functions of IQD proteins remain to be elucidated. In this study we show that IQD1 binds to multiple Arabidopsis CaM and CaM-like (CML) proteins in vitro and in yeast two-hybrid interaction assays. CaM overlay assays revealed moderate affinity of IQD1 to CaM2 (Kd ∼ 0.6 μm). Deletion mapping of IQD1 demonstrated the importance of the IQ67 domain for CaM2 binding in vitro, which is corroborated by interaction of the shortest IQD member, IQD20, with Arabidopsis CaM/CMLs in yeast. A genetic screen of a cDNA library identified Arabidopsis kinesin light chain-related protein-1 (KLCR1) as an IQD1 interactor. The subcellular localization of GFP-tagged IQD1 proteins to microtubules and the cell nucleus in transiently and stably transformed plant tissues (tobacco leaves and Arabidopsis seedlings) suggests direct interaction of IQD1 and KLCR1 in planta that is supported by GFP∼IQD1-dependent recruitment of RFP∼KLCR1 and RFP∼CaM2 to microtubules. Collectively, the prospect arises that IQD1 and related proteins provide Ca2+/CaM-regulated scaffolds for facilitating cellular transport of specific cargo along microtubular tracks via kinesin motor proteins.

Poeschl, Y.; Delker, C.; Trenner, J.; Ullrich, K.; Quint, M. & Grosse, I. Optimized probe masking for comparative transcriptomics of closely related species.<!--[if gte mso 9]><![endif]--><!--[if gte mso 9]><xml> Normal 0 21 false false false DE X-NONE X-NONE</xml><![endif]--><!--[if gte mso 9]><![endif]--><!--[if gte mso 10]> <style> /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Normale Tabelle"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-fareast-language:EN-US;}</style> <![endif]--> PLOS ONE 8, e78497, (2013) DOI: 10.1371/journal.pone.0078497

Microarrays are commonly applied to study the transcriptome of specific species. However, many available microarrays arerestricted to model organisms, and the design of custom microarrays for other species is often not feasible. Hence,transcriptomics approaches of non-model organisms as well as comparative transcriptomics studies among two or morespecies often make use of cost-intensive RNAseq studies or, alternatively, by hybridizing transcripts of a query species to amicroarray of a closely related species. When analyzing these cross-species microarray expression data, differences in thetranscriptome of the query species can cause problems, such as the following: (i) lower hybridization accuracy of probes dueto mismatches or deletions, (ii) probes binding multiple transcripts of different genes, and (iii) probes binding transcripts ofnon-orthologous genes. So far, methods for (i) exist, but these neglect (ii) and (iii). Here, we propose an approach forcomparative transcriptomics addressing problems (i) to (iii), which retains only transcript-specific probes binding transcriptsof orthologous genes. We apply this approach to an Arabidopsis lyrata expression data set measured on a microarraydesigned for Arabidopsis thaliana, and compare it to two alternative approaches, a sequence-based approach and a genomicDNA hybridization-based approach. We investigate the number of retained probe sets, and we validate the resultingexpression responses by qRT-PCR. We find that the proposed approach combines the benefit of sequence-based stringencyand accuracy while allowing the expression analysis of much more genes than the alternative sequence-based approach. Asan added benefit, the proposed approach requires probes to detect transcripts of orthologous genes only, which provides asuperior base for biological interpretation of the measured expression responses.
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