Papers by Lothar Altschmied
Acta Biologica Cracoviensia. Series Botanica. Supplement, 2005
Frontiers in Plant Science, 2021
Rapid cycle breeding uses transgenic early flowering plants as crossbreed parents to facilitate t... more Rapid cycle breeding uses transgenic early flowering plants as crossbreed parents to facilitate the shortening of breeding programs for perennial crops with long-lasting juvenility. Rapid cycle breeding in apple was established using the transgenic genotype T1190 expressing the BpMADS4 gene of silver birch. In this study, the genomes of T1190 and its non-transgenic wild-type PinS (F1-offspring of ‘Pinova’ and ‘Idared’) were sequenced by Illumina short-read sequencing in two separate experiments resulting in a mean sequencing depth of 182× for T1190 and 167× for PinS. The sequencing revealed 8,450 reads, which contain sequences of ≥20 bp identical to the plant transformation vector. These reads were assembled into 125 contigs, which were examined to see whether they contained transgenic insertions or if they are not using a five-step procedure. The sequence of one contig represents the known T-DNA insertion on chromosome 4 of T1190. The sequences of the remaining contigs were either ...
The Plant Cell, 2020
Whether, and to what extent, phenotypic evolution follows predictable genetic paths remains an im... more Whether, and to what extent, phenotypic evolution follows predictable genetic paths remains an important question in evolutionary biology. Convergent evolution of similar characters provides a unique opportunity to address this question. The transition to selfing and the associated changes in flower morphology are among the most prominent examples of repeated evolution in plants. In this study, we take advantage of the independent transitions to self-fertilization in the genus Capsella to compare the similarities between parallel modifications of floral traits and test for genetic and developmental constraints imposed on flower evolution in the context of the selfing syndrome. Capsella rubella and Capsella orientalis emerged independently but evolved almost identical flower characters. Not only is the evolutionary outcome identical but the same developmental strategies underlie the convergent reduction of flower size. This has been associated with convergent evolution of gene expression changes. The transcriptomic changes common to both selfing lineages are enriched in genes with low network connectivity and with organ-specific expression patterns. Comparative genetic mapping also suggests that, at least in the case of petal size evolution, these similarities have a similar genetic basis. Based on these results, we hypothesize that the limited availability of low-pleiotropy paths predetermines closely related species to similar evolutionary outcomes.
Grasses have varying inflorescence shapes; however, little is known about the genetic mechanisms ... more Grasses have varying inflorescence shapes; however, little is known about the genetic mechanisms specifying such shapes among tribes. We identified the grass-specific TCP transcription factor COMPOSITUM 1 (COM1) expressed in inflorescence meristematic boundaries of different grasses. COM1 specifies branch-inhibition in Triticeae (barley) versus branch-formation in non-Triticeae grasses. Analyses of cell size, cell walls and transcripts revealed barley COM1 regulates cell growth, affecting cell wall properties and signaling specifically in meristematic boundaries to establish identity of adjacent meristems.COM1acts upstream of the boundary geneLiguleless1and confers meristem identity partially independent of theCOM2pathway. Furthermore, COM1 is subject to purifying natural selection, thereby contributing to specification of the spike inflorescence shape. This meristem identity pathway has conceptual implications for both inflorescence evolution and molecular breeding in Triticeae.
The Plant Journal, 2019
SummaryRNA‐based processes play key roles in the regulation of eukaryotic gene expression. This i... more SummaryRNA‐based processes play key roles in the regulation of eukaryotic gene expression. This includes both the processing of pre‐mRNAs into mature mRNAs ready for translation and RNA‐based silencing processes, such as RNA‐directed DNA methylation (RdDM). Polyadenylation of pre‐mRNAs is one important step in their processing and is carried out by three functionally specialized canonical nuclear poly(A) polymerases in Arabidopsis thaliana. Null mutations in one of these, termed PAPS1, result in a male gametophytic defect. Using a fluorescence‐labelling strategy, we have characterized this defect in more detail using RNA and small‐RNA sequencing. In addition to global defects in the expression of pollen‐differentiation genes, paps1 null‐mutant pollen shows a strong overaccumulation of transposable element (TE) transcripts, yet a depletion of 21‐ and particularly 24‐nucleotide‐long short interfering RNAs (siRNAs) and microRNAs (miRNAs) targeting the corresponding TEs. Double‐mutant a...
The EMBO Journal, 1988
The tet operators of two naturally evolved tetracycline resistance determinants differ by a G-C t... more The tet operators of two naturally evolved tetracycline resistance determinants differ by a G-C to A T transition at the sixth base pair. This mutation prevents heterologous recognition of these tet operators by their respective two Tet repressor proteins. The amino acid side chains responsible for this sequence-specific distinction of operators were determined. For this purpose in vitro recombinants of the two tetR genes were constructed. Restriction sites were introduced by oligonucleotide-directed mutagenesis in both genes followed by the exchange of different coding segments between them. The encoded chimeric Tet repressor proteins were expressed and their operator recognition specificity was scored in vivo. Exchanging gradually smaller coding segments led fmally to a single amino acid exchange in both genes at position 4) of the primary structures. Each Tet repressor containing Thr at this position recognizes the G C operator while those with Ala recognize the A T operator regardless of the rest of the sequences. This result demonstrates clearly that the amino acid 40 of Tet repressor contacts and recognizes base pair 6 of tet operator. Sterical interference of the large Thr side chain with the methyl group of A T and a possible involvement of the hydroxyl in hydrogen bonding to the operator are discussed as the molecular basis of this differentiation between AT and G*C base pairs.
Plant physiology, Jan 25, 2018
Piriformospora indica, an endophytic root-colonizing fungus, efficiently promotes plant growth an... more Piriformospora indica, an endophytic root-colonizing fungus, efficiently promotes plant growth and induces resistance to abiotic stress and biotic diseases. The fungal cell wall extract induces cytoplasmic calcium [Ca2+]cyt elevation in host plant roots. Here, we show that an elici-tor-active cell wall moiety, released by P. indica into the medium, is cellotriose (CT). CT in-duces a mild defense-like response including the production of reactive oxygen species, changes in membrane potentials and the expression of genes involved in growth regulation and root development. CT based [Ca2+]cyt elevation in Arabidopsis roots does not require BAK1 coreceptor, or the putative Ca2+ channels TPC1, GLR3.3, -2.4 and -2.5 and operates synergistically with the elicitor chitin. We identified an ethylmethane-sulfonate-induced mu-tant ([Ca2+]cyt elevation mutant, cycam) impaired in response to CT, cellooligomers (n = 2, 4-7), but not to chitooligomers (n = 4-8) in roots. The mutant contains a single...
Frontiers in Plant Science, 2017
Unlike sexual reproduction, apomixis encompasses a number of reproductive strategies, which permi... more Unlike sexual reproduction, apomixis encompasses a number of reproductive strategies, which permit maternal genome inheritance without genetic recombination and syngamy. The key biological features of apomixis are the circumvention of meiosis (i.e., apomeiosis), the differentiation of unreduced embryo sacs and egg cells, and their autonomous development in functional embryos through parthenogenesis, and the formation of viable endosperm either via fertilization-independent means or following fertilization with a sperm cell. Despite the importance of apomixis for breeding of crop plants and although much research has been conducted to study this process, the genetic control of apomixis is still not well understood. Hypericum perforatum is becoming an attractive model system for the study of aposporous apomixis. Here we report results from a global gene expression analysis of H. perforatum pistils collected from sexual and aposporous plant accessions for the purpose of identifying genes, biological processes and molecular functions associated with the aposporous apomixis pathway. Across two developmental stages corresponding to the expression of aposporous apomeiosis and parthenogenesis in ovules, a total of 224 and 973 unigenes were found to be significantly up-and down-regulated with a fold change ≥ 2 in at least one comparison, respectively. Differentially expressed genes were enriched for multiple gene ontology (GO) terms, including cell cycle, DNA metabolic process, and single-organism cellular process. For molecular functions, the highest scores were recorded for GO terms associated with DNA binding, DNA (cytosine-5-)-methyltransferase activity and heterocyclic compound binding. As deregulation of single components of the sexual developmental pathway is believed to be a trigger of the apomictic reproductive program, all genes involved in sporogenesis, gametogenesis and response to hormonal stimuli were analyzed in great detail. Overall, our data suggest that phenotypic expression of apospory is concomitant with the modulation of key genes involved in the sexual reproductive pathway. Furthermore, based on gene annotation and co-expression, we underline a putative role of hormones and key actors playing in the RNA-directed DNA methylation pathway in regulating the developmental changes occurring during aposporous apomixis in H. perforatum.
Plant Physiology, 1997
Chloroplast subfractions were monitored for sodium dodecyl sulfate-stable proteases. Nine distinc... more Chloroplast subfractions were monitored for sodium dodecyl sulfate-stable proteases. Nine distinct activities in the molecular mass range from 14 to 66 kD have been detected. Five of the proteases associated with thylakoid membranes belong to the serine and cysteine types of proteases. These activities could be preserved and purified by a two-step electrophoresis procedure.
Planta, 2016
Main conclusion A novel annotated Chelidonium majus L. transcriptome database composed of 23,004 ... more Main conclusion A novel annotated Chelidonium majus L. transcriptome database composed of 23,004 unique coding sequences allowed to significantly improve the sensitivity of proteomic C. majus assessments, which showed novel defense-related proteins characteristic to its latex. To date, the composition of Chelidonium majus L. milky sap and biosynthesis of its components are poorly characterized. We, therefore, performed de novo sequencing and assembly of C. majus transcriptome using Illumina technology. Approximately, 119 Mb of raw sequence data was obtained. Assembly resulted in 107,088 contigs, with N50 of 1913 bp and N90 of 450 bp. Among 34,965 unique coding sequences (CDS), 23,004 obtained CDS database served as a basis for further proteomic analyses. The database was then used for the identification of proteins from C. majus milky sap, and whole plant extracts analyzed using liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) approach. Of about 334 different putative proteins were identified in C. majus milky sap and 1155 in C. majus whole plant extract. The quantitative comparative analysis confirmed that C. majus latex contains proteins connected with response to stress conditions and generation of precursor metabolites and energy. Notable proteins characteristic to latex include major latex protein (MLP, presumably belonging to Bet v1like superfamily), polyphenol oxidase (PPO, which could be responsible for browning of the sap after exposure to air), and enzymes responsible for anthocyanidin, phenylpropanoid, and alkaloid biosynthesis.
Plant Molecular Biology Reporter, 2016
Hypericum perforatum is a traditional medicinal plant used for various purposes since ancient tim... more Hypericum perforatum is a traditional medicinal plant used for various purposes since ancient times because of the valuable secondary metabolites. The genomic information for H. perforatum is limited and the regulatory networks of secondary metabolism are still unknown. The naphthodianthrone hypericin is the metabolite of our main interest. It is a red-colored photodynamic pigment localized in dark glands of some Hypericum species. High-throughput sequencing technology, especially RNA-Seq, followed by de novo assembly and analysis of differential gene expression provides an important tool for functional genomics of non-model organisms. It represents an opportunity of insight into dynamic biological processes including those of secondary metabolism. Transcriptome analysis followed by the analysis of differential gene expression of H. perforatum leaf tissues containing and lacking dark glands was performed to identify the genes involved in hypericin biosynthesis and to profile expression patterns in greater detail. A total of 18.53 G of cleaned read nucleotides were generated and assembled into 139,959 contigs with N50 of 1801 bp. Among them, 66,817 (47.74 %) contigs were annotated. Differentially expressed genes were discovered by comparison of dark glands with adjacent leaf tissue and contrasting inner part leaf tissue without dark glands. A total of 799 upregulated genes were found in the tissues containing dark glands and 263 enzymes were identified, including candidate genes of hypericin biosynthesis, especially the genes coding for polyketide synthases and those involved in defense reactions. This study determined candidate genes involved in hypericin biosynthesis providing a valuable source for perspective metabolic engineering of bioactive substances.
Handbook of Genome Research
... 1) Additional 63 bp compared with the original sequence 2) Genes with known or predicted func... more ... 1) Additional 63 bp compared with the original sequence 2) Genes with known or predicted function 3) No other data available other than the existence of an open reading frame with a start sequence and more than 100 codons 4) Data from http://tula.cifn.unam.mx ...
Essentials of Genomics and Bioinformatics
Chloroplast subfractions were monitored for sodium dodecyl sulfate-stable proteases. Nine distinc... more Chloroplast subfractions were monitored for sodium dodecyl sulfate-stable proteases. Nine distinct activities in the molecular mass range from 14 to 66 kD have been detected. Five of the proteases associated with thylakoid membranes belong to the serine and cysteine types of proteases. These activities could be preserved and purified by a two-step electrophoresis procedure. ~ ~ /
The Plant Cell, 2010
Immunity of plants triggered by pathogen-associated molecular patterns (PAMPs) is based on the ex... more Immunity of plants triggered by pathogen-associated molecular patterns (PAMPs) is based on the execution of an evolutionarily conserved defense response that includes the accumulation of pathogenesis-related (PR) proteins as well as multiple other defenses. The most abundant PR transcript of barley (Hordeum vulgare) leaf epidermis attacked by the powdery mildew fungus Blumeria graminis f. sp hordei encodes the germin-like protein GER4, which has superoxide dismutase activity and functions in PAMP-triggered immunity. Here, we show that barley GER4 is encoded by a dense cluster of tandemly duplicated genes (GER4a-h) that underwent several cycles of duplication. The genomic organization of the GER4 locus also provides evidence for repeated gene birth and death cycles. The GER4 promoters contain multiple WRKY factor binding sites (W-boxes) preferentially located in promoter fragments that were exchanged between subfamily members by gene conversion. Mutational analysis of TATA-box proxim...
Sexual Plant Reproduction, 2001
The 'Salmon' system of wheat comprises three isogenic alloplasmic lines with either zygotic (aS) ... more The 'Salmon' system of wheat comprises three isogenic alloplasmic lines with either zygotic (aS) or autonomous, fertilisation-independent (cS kS) embryo development. While the initiation of embryogenesis from the isolated sexual egg cell depends on in vitro fertilisation, the corresponding parthenogenetic egg cell develops into an early embryo without fertilisation. This demonstrates that parthenogenesis is an inherent feature of the isolated egg cell. Based on this observation, we have constructed egg-cell-specific cDNA libraries and report first results of a sequencing project aimed at the isolation of putative egg-cell-specific and parthenogenesis-related genes.
Planta, 2004
In Arabidopsis thaliana (L.) Heynh. the seed-specific transcription factors ABI3 and FUS3 have ke... more In Arabidopsis thaliana (L.) Heynh. the seed-specific transcription factors ABI3 and FUS3 have key regulatory functions during the development of mature seeds. The highly conserved RY motif [DNA motif CATGCA(TG)], present in many seed-specific promoters, is an essential target of both regulators. Here we show that, in vitro, the full-length ABI3 protein, as well as FUS3 protein, is able to bind to RY-DNA and that the B3 domains of both transcription factors are necessary and sufficient for the specific interaction with the RY element. Flanking sequences of the RY motif modulate the binding, but the presence of an RY sequence alone allows the specific interaction of ABI3 and FUS3 with the target in vitro. Transcriptional activity of ABI3 and FUS3, measured by transient promoter activation, requires the B3 DNA-binding domain and an activation domain. In addition to the known N-terminal-located activation domain, a second transcription activation domain was found in the B1 region of ABI3.
Planta, 1998
The Clp proteases represent a large, ancient ATP-dependent protease family which in higher plants... more The Clp proteases represent a large, ancient ATP-dependent protease family which in higher plants is known to be located in chloroplasts. The soluble, presumably multisubunit, enzyme of the organelle stroma is of dual genetic origin. It consists of a nuclear-encoded, regulatory subunit ClpC, which is an ATPase, and a plastid-encoded proteolytic subunit ClpP, which is a serine protease. An additional, nuclear-encoded proteolytic subunit resembling ClpP has been recently reported from tomato (Schaller and Ryan, 1995 plant gene Register 95±00). We demonstrate that in both tomato Lycopersicon esculentum Mill. and Arabidopsis thaliana, (L.) Heynh. the nuclear-encoded ClpP (nClpP) is made as a precursor molecule that can be imported into isolated intact chloroplasts of spinach (Spinacia oleracea L.) and processed in two or three steps, respectively, to the size of the authentic protein. Furthermore, both gel electrophoresis under non-denaturing conditions and size-exclusion chromatography veri®ed that the three proteins can form distinct heteromeric supramolecular complexes of approximately 860, 1380 and 1700 kDa (probably also of 600 kDa) molecular mass. The size ranges of the former two are reminiscent of those of Clp complexes described from Escherichia coli. In addition, various complexes between 160 and 560 kDa are detectable with the individual components. Both the processing``intermediates'' and the mature nClpP are found in assembled form.
Planta, 1997
Four distinct integration/translocation routes into/across thylakoid membranes have recently been... more Four distinct integration/translocation routes into/across thylakoid membranes have recently been deduced for nuclear-encoded polypeptides of the photosynthetic membrane. Corresponding information for the plastid-encoded protein complement is lacking. We have investigated this aspect with in-organello assays employing chimeric constructs generated with codoncorrect cassettes for genes of plastid-encoded thylakoid proteins, and appropriate transit peptides from six nuclear genes, representing three targeting classes, as a strategy. The three major plastid-encoded components of the cytochrome b (6)f complex, namely pre-apocytochrome f, (including apocytochrome f, and pre-apocytochrome f lacking the C-terminal transmembrane segment), cytochrome b(6), and subunit IV, which differ in the number of their transmembrane segments, were studied. Import into chloroplasts could be observed in all instances but with relatively low efficiency. Thylakoid integration can occurr post-translationally, but only components with secretory/secretory pathway (SEC)-route-specific epitopes were correctly assembled with the cytochrome complex, or competed with this process. Inhibitor studies were consistent with these findings. Imported cytochrome b(6) and subunit IV operated with uncleaved targeting signals for thylakoid integration. The corresponding determinant for cytochrome f is its signal peptide; its C-terminal hydrophobic segment did not, or did not appreciably, contribute to this process. The N-termini of cytochrome b(6) and subunit IV appear to reside on the same (lumenal) side of the membrane, consistent with the currently favored four-helix model for the cytochrome, but in disagreement with the topography proposed for both components. The impact of the findings for protein routing, including for applied approaches such as compartment-alien transformation, is discussed.
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Papers by Lothar Altschmied