bluuebunny/crossref_metadata_2025 huggingface dataset:
RNA polymerase I transcription and pre-rRNA processing are linked by specific SSU processome components
Authors: Gallagher Jennifer E.G. , Dunbar David A. , Granneman Sander , Mitchell Brianna M. , Osheim Yvonne , Beyer Ann L. , Baserga Susan J.
Published: October 2004

Sequential events in macromolecular biosynthesis are often elegantly coordinated. The small ribosomal subunit (SSU) processome is a large ribonucleoprotein (RNP) required for processing of precursors to the small subunit RNA, the 18S, of the ribosome. We have found that a subcomplex of SSU processome proteins, the t-Utps, is also required for optimal rRNA transcription in vivo in the yeast Saccharomyces cerevisiae. The t-Utps are ribosomal chromatin (r-chromatin)-associated, and they exist in a complex in the absence of the U3 snoRNA. Transcription is required neither for the formation of the subcomplex nor for its r-chromatin association. The t-Utps are associated with the pre-18S rRNAs independent of the presence of the U3 snoRNA. This association may thus represent an early step in the formation of the SSU processome. Our results indicate that rRNA transcription and pre-rRNA processing are coordinated via specific components of the SSU processome.
Telomerase- and recombination-independent immortalization of budding yeast
Authors: Maringele Laura , Lydall David
Published: October 2004

It is generally assumed that there are only two ways to maintain the ends of chromosomes in yeast and mammalian nuclei: telomerase and recombination. Without telomerase and recombination, cells enter senescence, a state of permanent growth arrest. We found that the decisive role in preventing senescent budding yeast cells from dividing is played by the Exo1 nuclease. In the absence of Exo1, telomerase- and recombination-defective yeast can resume cell cycle progression, despite degradation of telomeric regions from many chromosomes. As degradation progresses toward internal chromosomal regions, a progressive decrease in viability would be expected, caused by loss of essential genes. However, this was not the case. We demonstrate that extensive degradation and loss of essential genes can be efficiently prevented through a little-studied mechanism of DNA double-strand-break repair, in which short DNA palindromes induce formation of large DNA palindromes. For the first time, we show that large palindromes form as a natural consequence of postsenescence growth and that they become essential for immortalization in the absence of telomerase activity.
The active spatial organization of the β-globin locus requires the transcription factor EKLF
Authors: Drissen Roy , Palstra Robert-Jan , Gillemans Nynke , Splinter Erik , Grosveld Frank , Philipsen Sjaak , de Laat Wouter
Published: October 2004

Three-dimensional organization of a gene locus is important for its regulation, as recently demonstrated for the β-globin locus. When actively expressed, the cis-regulatory elements of the β-globin locus are in proximity in the nuclear space, forming a compartment termed the Active Chromatin Hub (ACH). However, it is unknown which proteins are involved in ACH formation. Here, we show that EKLF, an erythroid transcription factor required for adult β-globin gene transcription, is also required for ACH formation. We conclude that transcription factors can play an essential role in the three-dimensional organization of gene loci.
A nuclear isoform of the focal adhesion LIM-domain protein Trip6 integrates activating and repressing signals at AP-1- and NF-κB-regulated promoters
Authors: Kassel Olivier , Schneider Sandra , Heilbock Christine , Litfin Margarethe , Göttlicher Martin , Herrlich Peter
Published: October 2004

Glucocorticoid receptor (GR)-mediated transrepression of the transcription factors AP-1 and NF-κB, responsible for most of the anti-inflammatory effects of glucocorticoids, is initiated by the tethering of GR to the promoters of target genes. We report that this tethering is mediated by a nuclear isoform of the focal adhesion LIM domain protein Trip6. Trip6 functions as a coactivator for both AP-1 and NF-κB. As shown by chromatin immunoprecipitation, Trip6 is recruited to the promoters of target genes together with AP-1 or NF-κB. In the presence of glucocorticoids, GR joins the Trip6 complex. Reducing the level of Trip6 by RNA interference or abolishing its interaction with GR by dominant-negative mutation eliminates transrepression. We propose that GR tethering to the target promoter through Trip6 forms the basis of transrepression, and that Trip6 exerts its nuclear functions by acting as a molecular platform, enabling target promoters to integrate activating or repressing signals.
Analysis of Small Human Proteins Reveals the Translation of Upstream Open Reading Frames of mRNAs
Authors: Oyama Masaaki , Itagaki Chiharu , Hata Hiroko , Suzuki Yutaka , Izumi Tomonori , Natsume Tohru , Isobe Toshiaki , Sugano Sumio
Published: October 2004

To find novel short coding sequences from accumulated full-length cDNA sequences, proteomic analysis of small proteins expressed in human leukemia K562 cells was performed using high-resolution nanoflow liquid chromatography coupled with electrospray ionization tandem mass spectrometry. Our analysis led to the identification of 54 proteins not more than 100 amino acids in length, including four novel ones. These novel short coding sequences were all located upstream of the longest open reading frame (ORF) of the corresponding cDNA. Our findings indicate that the translation of short ORFs occurs in vivo whether or not there exists a longer coding region in the downstream of the mRNA. This investigation provides the first direct evidence of translation of upstream ORFs in human cells, which could greatly change the current outline of the human proteome.
High-Throughput Generation of P. falciparum Functional Molecules by Recombinational Cloning
Authors: Aguiar João Carlos , LaBaer Joshua , Blair Peter L. , Shamailova Victoria Y. , Koundinya Malvika , Russell Joshua A. , Huang Fengying , Mar Wenhong , Anthony Robert M. , Witney Adam , Caruana Sonia R. , Brizuela Leonardo , Sacci John B. , Hoffman Stephen L. , Carucci Daniel J.
Published: October 2004

Large-scale functional genomics studies for malaria vaccine and drug development will depend on the generation of molecular tools to study protein expression. We examined the feasibility of a high-throughput cloning approach using the Gateway system to create a large set of expression clones encoding Plasmodium falciparum single-exon genes. Master clones and their ORFs were transferred en masse to multiple expression vectors. Target genes (n = 303) were selected using specific sets of criteria, including stage expression and secondary structure. Upon screening four colonies per capture reaction, we achieved 84% cloning efficiency. The genes were subcloned in parallel into three expression vectors: a DNA vaccine vector and two protein expression vectors. These transfers yielded a 100% success rate without any observed recombination based on single colony screening. The functional expression of 95 genes was evaluated in mice with DNA vaccine constructs to generate antibody against various stages of the parasite. From these, 19 induced antibody titers against the erythrocytic stages and three against sporozoite stages. We have overcome the potential limitation of producing large P. falciparum clone sets in multiple expression vectors. This approach represents a powerful technique for the production of molecular reagents for genome-wide functional analysis of the P. falciparum genome and will provide for a resource for the malaria resource community distributed through public repositories.
Generation of the Brucella melitensis ORFeome Version 1.1: Figure 1
Authors: Dricot Amélie , Rual Jean-François , Lamesch Philippe , Bertin Nicolas , Dupuy Denis , Hao Tong , Lambert Christophe , Hallez Régis , Delroisse Jean-Marc , Vandenhaute Jean , Lopez-Goñi Ignacio , Moriyon Ignacio , Garcia-Lobo Juan M. , Sangari Félix J. , MacMillan Alastair P. , Cutler Sally J. , Whatmore Adrian M. , Bozak Stephanie , Sequerra Reynaldo , Doucette-Stamm Lynn , Vidal Marc , Hill David E. , Letesson Jean-Jacques , De Bolle Xavier
Published: October 2004

The bacteria of the Brucella genus are responsible for a worldwide zoonosis called brucellosis. They belong to the α-proteobacteria group, as many other bacteria that live in close association with a eukaryotic host. Importantly, the Brucellae are mainly intracellular pathogens, and the molecular mechanisms of their virulence are still poorly understood. Using the complete genome sequence of Brucella melitensis, we generated a database of protein-coding open reading frames (ORFs) and constructed an ORFeome library of 3091 Gateway Entry clones, each containing a defined ORF. This first version of the Brucella ORFeome (v1.1) provides the coding sequences in a user-friendly format amenable to high-throughput functional genomic and proteomic experiments, as the ORFs are conveniently transferable from the Entry clones to various Expression vectors by recombinational cloning. The cloning of the Brucella ORFeome v1.1 should help to provide a better understanding of the molecular mechanisms of virulence, including the identification of bacterial protein-protein interactions, but also interactions between bacterial effectors and their host's targets.
Analysis of Human mRNAs With the Reference Genome Sequence Reveals Potential Errors, Polymorphisms, and RNA Editing
Authors: Furey Terrence S. , Diekhans Mark , Lu Yontao , Graves Tina A. , Oddy Lachlan , Randall-Maher Jennifer , Hillier LaDeana W. , Wilson Richard K. , Haussler David
Published: October 2004

The NCBI Reference Sequence (RefSeq) project and the NIH Mammalian Gene Collection (MGC) together define a set of ∼30,000 nonredundant human mRNA sequences with identified coding regions representing 17,000 distinct loci. These high-quality mRNA sequences allow for the identification of transcribed regions in the human genome sequence, and many researchers accept them as the correct representation of each defined gene sequence. Computational comparison of these mRNA sequences and the recently published essentially finished human genome sequence reveals several thousand undocumented nonsynonymous substitution and frame shift discrepancies between the two resources. Additional analysis is undertaken to verify that the euchromatic human genome is sufficiently complete—containing nearly the whole mRNA collection, thus allowing for a comprehensive analysis to be undertaken. Many of the discrepancies will prove to be genuine polymorphisms in the human population, somatic cell genomic variants, or examples of RNA editing. It is observed that the genome sequence variant has significant additional support from other mRNAs and ESTs, almost four times more often than does the mRNA variant, suggesting that the genome sequence is more accurate. In ∼15% of these cases, there is substantial support for both variants, suggestive of an undocumented polymorphism. An initial screening against a 24-individual genomic DNA diversity panel verified 60% of a small set of potential single nucleotide polymorphisms from which successful results could be obtained. We also find statistical evidence that a few of these discrepancies are due to RNA editing. Overall, these results suggest that the mRNA collections may contain a substantial number of errors. For current and future mRNA collections, it may be prudent to fully reconcile each genome sequence discrepancy, classifying each as a polymorphism, site of RNA editing or somatic cell variation, or genome sequence error.
Systematic Recovery and Analysis of Full-ORF Human cDNA Clones
Authors: Baross Ágnes , Butterfield Yaron S.N. , Coughlin Shaun M. , Zeng Thomas , Griffith Malachi , Griffith Obi L. , Petrescu Anca S. , Smailus Duane E. , Khattra Jaswinder , McDonald Helen L. , McKay Sheldon J. , Moksa Michelle , Holt Robert A. , Marra Marco A.
Published: October 2004

The Mammalian Gene Collection (MGC) consortium (http://mgc.nci.nih.gov) seeks to establish publicly available collections of full-ORF cDNAs for several organisms of significance to biomedical research, including human. To date over 15,200 human cDNA clones containing full-length open reading frames (ORFs) have been identified via systematic expressed sequence tag (EST) analysis of a diverse set of cDNA libraries; however, further systematic EST analysis is no longer an efficient method for identifying new cDNAs. As part of our involvement in the MGC program, we have developed a scalable method for targeted recovery of cDNA clones to facilitate recovery of genes absent from the MGC collection. First, cDNA is synthesized from various RNAs, followed by polymerase chain reaction (PCR) amplification of transcripts in 96-well plates using gene-specific primer pairs flanking the ORFs. Amplicons are cloned into a sequencing vector, and full-length sequences are obtained. Sequences are processed and assembled using Phred and Phrap, and analyzed using Consed and a number of bioinformatics methods we have developed. Sequences are compared with the Reference Sequence (RefSeq) database, and validation of sequence discrepancies is attempted using other sequence databases including dbEST and dbSNP. Clones with identical sequence to RefSeq or containing only validated changes will become part of the MGC human gene collection. Clones containing novel splice variants or polymorphisms have also been identified. Our approach to clone recovery, applied at large scale, has the potential to recover many and possibly most of the genes absent from the MGC collection.
The Pseudomonas aeruginosa PA01 Gene Collection
Authors: LaBaer Joshua , Qiu QingQing , Anumanthan Anukanth , Mar Wenhong , Zuo Dongmei , Murthy T.V.S. , Taycher Helen , Halleck Allison , Hainsworth Eugenie , Lory Stephen , Brizuela Leonardo
Published: October 2004

Pseudomonas aeruginosa, a common inhabitant of soil and water, is an opportunistic pathogen of growing clinical relevance. Its genome, one of the largest among bacteria [5570 open reading frames (ORFs)] approaches that of simple eukaryotes. We have constructed a comprehensive gene collection for this organism utilizing the annotated genome of P. aeruginosa PA01 and a highly automated and laboratory information management system (LIMS)-supported production line. All the individual ORFs have been successfully PCR-amplified and cloned into a recombination-based cloning system. We have isolated and archived four independent isolates of each individual ORF. Full sequence analysis of the first isolate for one-third of the ORFs in the collection has been completed. We used two sets of genes from this repository for high-throughput expression and purification of recombinant proteins in different systems. The purified proteins have been used to set up biochemical and immunological assays directed towards characterization of histidine kinases and identification of bacterial proteins involved in the immune response of cystic fibrosis patients. This gene repository provides a powerful tool for proteome- and genome-scale research of this organism, and the strategies adopted to generate this repository serve as a model for building clone sets for other bacteria.
A First Version of the Caenorhabditis elegans Promoterome
Authors: Dupuy Denis , Li Qian-Ru , Deplancke Bart , Boxem Mike , Hao Tong , Lamesch Philippe , Sequerra Reynaldo , Bosak Stephanie , Doucette-Stamm Lynn , Hope Ian A. , Hill David E. , Walhout Albertha J.M. , Vidal Marc
Published: October 2004

An important aspect of the development of systems biology approaches in metazoans is the characterization of expression patterns of nearly all genes predicted from genome sequences. Such “localizome” maps should provide information on where (in what cells or tissues) and when (at what stage of development or under what conditions) genes are expressed. They should also indicate in what cellular compartments the corresponding proteins are localized. Caenorhabditis elegans is particularly suited for the development of a localizome map since all its 959 adult somatic cells can be visualized by microscopy, and its cell lineage has been completely described. Here we address one of the challenges of C. elegans localizome mapping projects: that of obtaining a genome-wide resource of C. elegans promoters needed to generate transgenic animals expressing localization markers such as the green fluorescent protein (GFP). To ensure high flexibility for future uses, we utilized the newly developed MultiSite Gateway system. We generated and validated “version 1.1” of the Promoterome: a resource of ∼6000 C. elegans promoters. These promoters can be transferred easily into various Gateway Destination vectors to drive expression of markers such as GFP, alone (promoter::GFP constructs), or in fusion with protein-encoding open reading frames available in ORFeome resources (promoter::ORF::GFP).
High-Throughput Expression of C. elegans Proteins
Authors: Luan Chi-Hao , Qiu Shihong , Finley James B. , Carson Mike , Gray Rita J. , Huang Wenying , Johnson David , Tsao Jun , Reboul Jérôme , Vaglio Philippe , Hill David E. , Vidal Marc , DeLucas Lawrence J. , Luo Ming
Published: October 2004

Proteome-scale studies of protein three-dimensional structures should provide valuable information for both investigating basic biology and developing therapeutics. Critical for these endeavors is the expression of recombinant proteins. We selected Caenorhabditis elegans as our model organism in a structural proteomics initiative because of the high quality of its genome sequence and the availability of its ORFeome, protein-encoding open reading frames (ORFs), in a flexible recombinational cloning format. We developed a robotic pipeline for recombinant protein expression, applying the Gateway cloning/expression technology and utilizing a stepwise automation strategy on an integrated robotic platform. Using the pipeline, we have carried out heterologous protein expression experiments on 10,167 ORFs of C. elegans. With one expression vector and one Escherichia coli strain, protein expression was observed for 4854 ORFs, and 1536 were soluble. Bioinformatics analysis of the data indicates that protein hydrophobicity is a key determining factor for an ORF to yield a soluble expression product. This protein expression effort has investigated the largest number of genes in any organism to date. The pipeline described here is applicable to high-throughput expression of recombinant proteins for other species, both prokaryotic and eukaryotic, provided that ORFeome resources become available.
Many Paths to Many Clones: A Comparative Look at High-Throughput Cloning Methods
Authors: Marsischky Gerald , LaBaer Joshua
Published: October 2004

The creation of genome-scale clone resources is a difficult and costly process, making it essential to maximize the efficiency of each step of clone creation. In this review, we compare the available commercial and open-source recombinational cloning methods with regard to their use in creating comprehensive open reading frame (ORF) clone collections with an emphasis on the properties requisite to use in a high-throughput setting. The most efficient strategy to the creation of ORF clone resources is to build a master clone collection that serves as a quality validated source for producing collections of expression clones. We examine the methods for recombinational cloning available for both the creation of master clones and their conversion into expression clones. Alternative approaches to creating clones involving mixing of cloning methods, including gap-repair cloning, are also explored.
From ORFeomes to Protein Interaction Maps in Viruses
Authors: Uetz Peter , Rajagopala Seesandra V. , Dong Yu-An , Haas Jürgen
Published: October 2004

Although cloned viral ORFeomes are particularly well suited for genome-wide interaction mapping due to the limited size of viral genomes, only a few such studies have been published. Here, we summarize virus interaction mapping projects involving vaccinia virus, hepatitis C virus (HCV), potato virus A (PVA), pea seed-borne mosaic virus (PSbMV), and bacteriophage T7, as well as some projects in progress. The studies reported suggest that virus-specific coding and replication strategies must be taken into account to yield accurate numbers of protein interactions. In particular, the number of false negatives can be significant for RNA viruses expressing precursor polyproteins (because interactions between full-length mature proteins are often not detected due to incorrect processing) and for viruses replicating in the cytoplasm whose transcripts have not been selected for splicing signals. In conclusion, the studies on viral protein interaction maps suggest that cloned pathogen ORFeomes will contribute to a holistic picture of the pathogenesis of infectious diseases and are ideal starting points for new approaches in systems biology. Both viral ORFeome and interaction mapping projects are being documented on our Web site (http://itgmv1.fzk.de/www/itg/uetz/virus/).
An ORFeome-based Analysis of Human Transcription Factor Genes and the Construction of a Microarray to Interrogate Their Expression
Authors: Messina David N. , Glasscock Jarret , Gish Warren , Lovett Michael
Published: October 2004

Transcription factors (TFs) are essential regulators of gene expression, and mutated TF genes have been shown to cause numerous human genetic diseases. Yet to date, no single, comprehensive database of human TFs exists. In this work, we describe the collection of an essentially complete set of TF genes from one depiction of the human ORFeome, and the design of a microarray to interrogate their expression. Taking 1468 known TFs from TRANSFAC, InterPro, and FlyBase, we used this seed set to search the ScriptSure human transcriptome database for additional genes. ScriptSure's genome-anchored transcript clusters allowed us to work with a nonredundant high-quality representation of the human transcriptome. We used a high-stringency similarity search by using BLASTN, and a protein motif search of the human ORFeome by using hidden Markov models of DNA-binding domains known to occur exclusively or primarily in TFs. Four hundred ninety-four additional TF genes were identified in the overlap between the two searches, bringing our estimate of the total number of human TFs to 1962. Zinc finger genes are by far the most abundant family (762 members), followed by homeobox (199 members) and basic helix-loop-helix genes (117 members). We designed a microarray of 50-mer oligonucleotide probes targeted to a unique region of the coding sequence of each gene. We have successfully used this microarray to interrogate TF gene expression in species as diverse as chickens and mice, as well as in humans.
Human ORFeome Version 1.1: A Platform for Reverse Proteomics
Authors: Rual Jean-François , Hirozane-Kishikawa Tomoko , Hao Tong , Bertin Nicolas , Li Siming , Dricot Amélie , Li Ning , Rosenberg Jennifer , Lamesch Philippe , Vidalain Pierre-Olivier , Clingingsmith Tracey R. , Hartley James L. , Esposito Dominic , Cheo David , Moore Troy , Simmons Blake , Sequerra Reynaldo , Bosak Stephanie , Doucette-Stamm Lynn , Le Peuch Christian , Vandenhaute Jean , Cusick Michael E. , Albala Joanna S. , Hill David E. , Vidal Marc
Published: October 2004

The advent of systems biology necessitates the cloning of nearly entire sets of protein-encoding open reading frames (ORFs), or ORFeomes, to allow functional studies of the corresponding proteomes. Here, we describe the generation of a first version of the human ORFeome using a newly improved Gateway recombinational cloning approach. Using the Mammalian Gene Collection (MGC) resource as a starting point, we report the successful cloning of 8076 human ORFs, representing at least 7263 human genes, as mini-pools of PCR-amplified products. These were assembled into the human ORFeome version 1.1 (hORFeome v1.1) collection. After assessing the overall quality of this version, we describe the use of hORFeome v1.1 for heterologous protein expression in two different expression systems at proteome scale. The hORFeome v1.1 represents a central resource for the cloning of large sets of human ORFs in various settings for functional proteomics of many types, and will serve as the foundation for subsequent improved versions of the human ORFeome.
Use of Phenylboronic Acids to Investigate Boron Function in Plants. Possible Role of Boron in Transvacuolar Cytoplasmic Strands and Cell-to-Wall Adhesion
Authors: Bassil Elias , Hu Hening , Brown Patrick H.
Published: October 2004

The only defined physiological role of boron in plants is as a cross-linking molecule involving reversible covalent bonds with cis-diols on either side of borate. Boronic acids, which form the same reversible bonds with cis-diols but cannot cross-link two molecules, were used to selectively disrupt boron function in plants. In cultured tobacco (Nicotiana tabacum cv BY-2) cells, addition of boronic acids caused the disruption of cytoplasmic strands and cell-to-cell wall detachment. The effect of the boronic acids could be relieved by the addition of boron-complexing sugars and was proportional to the boronic acid-binding strength of the sugar. Experiments with germinating petunia (Petunia hybrida) pollen and boronate-affinity chromatography showed that boronic acids and boron compete for the same binding sites. The boronic acids appear to specifically disrupt or prevent borate-dependent cross-links important for the structural integrity of the cell, including the organization of transvacuolar cytoplasmic strands. Boron likely plays a structural role in the plant cytoskeleton. We conclude that boronic acids can be used to rapidly and reversibly induce boron deficiency-like responses and therefore are useful tools for investigating boron function in plants.
Utility of Different Gene Enrichment Approaches Toward Identifying and Sequencing the Maize Gene Space
Authors: Springer Nathan Michael , Xu Xiequn , Barbazuk W. Brad
Published: October 2004

Maize (Zea mays) possesses a large, highly repetitive genome, and subsequently a number of reduced-representation sequencing approaches have been used to try and enrich for gene space while eluding difficulties associated with repetitive DNA. This article documents the ability of publicly available maize expressed sequence tag and Genome Survey Sequences (GSSs; many of which were isolated through the use of reduced representation techniques) to recognize and provide coverage of 78 maize full-length cDNAs (FLCs). All 78 FLCs in the dataset were identified by at least three GSSs, indicating that the majority of maize genes have been identified by at least one currently available GSS. Both methyl-filtration and high-Cot enrichment methods provided a 7- to 8-fold increase in gene discovery rates as compared to random sequencing. The available maize GSSs aligned to 75% of the FLC nucleotides used to perform searches, while the expressed sequence tag sequences aligned to 73% of the nucleotides. Our data suggest that at least approximately 95% of maize genes have been tagged by at least one GSS. While the GSSs are very effective for gene identification, relatively few (18%) of the FLCs are completely represented by GSSs. Analysis of the overlap of coverage and bias due to position within a gene suggest that RescueMu, methyl-filtration, and high-Cot methods are at least partially nonredundant.
Expression Profiling inMedicago truncatulaIdentifies More Than 750 Genes Differentially Expressed during Nodulation, Including Many Potential Regulators of the Symbiotic Program
Authors: El Yahyaoui Fikri , Küster Helge , Ben Amor Besma , Hohnjec Natalija , Pühler Alfred , Becker Anke , Gouzy Jérôme , Vernié Tatiana , Gough Clare , Niebel Andreas , Godiard Laurence , Gamas Pascal
Published: October 2004

In this study, we describe a large-scale expression-profiling approach to identify genes differentially regulated during the symbiotic interaction between the model legume Medicago truncatula and the nitrogen-fixing bacterium Sinorhizobium meliloti. Macro- and microarrays containing about 6,000 probes were generated on the basis of three cDNA libraries dedicated to the study of root symbiotic interactions. The experiments performed on wild-type and symbiotic mutant material led us to identify a set of 756 genes either up- or down-regulated at different stages of the nodulation process. Among these, 41 known nodulation marker genes were up-regulated as expected, suggesting that we have identified hundreds of new nodulation marker genes. We discuss the possible involvement of this wide range of genes in various aspects of the symbiotic interaction, such as bacterial infection, nodule formation and functioning, and defense responses. Importantly, we found at least 13 genes that are good candidates to play a role in the regulation of the symbiotic program. This represents substantial progress toward a better understanding of this complex developmental program.
Structure and Mutational Analysis of a Plant Mitochondrial Nucleoside Diphosphate Kinase. Identification of Residues Involved in Serine Phosphorylation and Oligomerization
Authors: Johansson Monika , MacKenzie-Hose Alasdair , Andersson Inger , Knorpp Carina
Published: October 2004

We report the first crystal structure of a plant (Pisum sativum L. cv Oregon sugarpod) mitochondrial nucleoside diphosphate kinase. Similar to other eukaryotic nucleoside diphosphate kinases, the plant enzyme is a hexamer; the six monomers in the asymmetric unit are arranged as trimers of dimers. Different functions of the kinase have been correlated with the oligomeric structure and the phosphorylation of Ser residues. We show that the occurrence of Ser autophosphorylation depends on enzymatic activity. The mutation of the strictly conserved Ser-119 to Ala reduced the Ser phosphorylation to about one-half of that observed in wild type with only a modest change of enzyme activity. We also show that mutating another strictly conserved Ser, Ser-69, to Ala reduces the enzyme activity to 6% and 14% of wild-type using dCDP and dTDP as acceptors, respectively. Changes in the oligomerization pattern of the S69A mutant were observed by cross-linking experiments. A reduction in trimer formation and a change in the dimer interaction could be detected with a concomitant increase of tetramers. We conclude that the S69 mutant is involved in the stabilization of the oligomeric state of this plant nucleoside diphosphate kinase.
Comparative Sequence Analysis of the Region Harboring the Hardness Locus in Barley and Its Colinear Region in Rice
Authors: Caldwell Katherine S. , Langridge Peter , Powell Wayne
Published: October 2004

The ancestral shared synteny concept has been advocated as an approach to positionally clone genes from complex genomes. However, the unified grass genome model and the study of grasses as a single syntenic genome is a topic of considerable controversy. Hence, more quantitative studies of cereal colinearity at the sequence level are required. This study compared a contiguous 300-kb sequence of the barley (Hordeum vulgare) genome with the colinear region in rice (Oryza sativa). The barley sequence harbors genes involved in endosperm texture, which may be the subject of distinctive evolutionary forces and is located at the extreme telomeric end of the short arm of chromosome 5H. Comparative sequence analysis revealed the presence of five orthologous genes and a complex, postspeciation evolutionary history involving small chromosomal rearrangements, a translocation, numerous gene duplications, and extensive transposon insertion. Discrepancies in gene content and microcolinearity indicate that caution should be exercised in the use of rice as a surrogate for map-based cloning of genes from large genome cereals such as barley.
Production of Reactive Oxygen Intermediates (O2
˙−, H2O2, and ˙OH) by Maize Roots and Their Role in Wall Loosening and Elongation Growth
Authors: Liszkay Anja , van der Zalm Esther , Schopfer Peter
Published: October 2004

Cell extension in the growing zone of plant roots typically takes place with a maximum local growth rate of 50% length increase per hour. The biochemical mechanism of this dramatic growth process is still poorly understood. Here we test the hypothesis that the wall-loosening reaction controlling root elongation is effected by the production of reactive oxygen intermediates, initiated by a NAD(P)H oxidase-catalyzed formation of superoxide radicals (O2  ˙−) at the plasma membrane and culminating in the generation of polysaccharide-cleaving hydroxyl radicals (˙OH) by cell wall peroxidase. The following results were obtained using primary roots of maize (Zea mays) seedlings as experimental material. (1) Production of O2  ˙−, H2O2, and ˙OH can be demonstrated in the growing zone using specific histochemical assays and electron paramagnetic resonance spectroscopy. (2) Auxin-induced inhibition of growth is accompanied by a reduction of O2  ˙− production. (3) Experimental generation of ˙OH in the cell walls with the Fenton reaction causes wall loosening (cell wall creep), specifically in the growing zone. Alternatively, wall loosening can be induced by ˙OH produced by endogenous cell wall peroxidase in the presence of NADH and H2O2. (4) Inhibition of endogenous ˙OH formation by O2  ˙− or ˙OH scavengers, or inhibitors of NAD(P)H oxidase or peroxidase activity, suppress elongation growth. These results show that juvenile root cells transiently express the ability to generate ˙OH, and to respond to ˙OH by wall loosening, in passing through the growing zone. Moreover, inhibitor studies indicate that ˙OH formation is essential for normal root growth.
Gene Expression Profiling Reflects Physiological Processes in Salt Acclimation of Synechocystis sp. Strain PCC 6803
Authors: Marin Kay , Kanesaki Yu , Los Dmitry A. , Murata Norio , Suzuki Iwane , Hagemann Martin
Published: October 2004

The kinetics of genome-wide responses of gene expression during the acclimation of cells of Synechocystis sp. PCC 6803 to salt stress were followed by DNA-microarray technique and compared to changes in main physiological parameters. During the first 30 min of salt stress, about 240 genes became induced higher than 3-fold, while about 140 genes were repressed. However, most changes in gene expression were only transient and observed among genes for hypothetical proteins. At 24 h after onset of salt stress conditions, the expression of only 39 genes remained significantly enhanced. Among them, many genes that encode proteins essential for salt acclimation were detected, while only a small number of genes for hypothetical proteins remained activated. Following the expression of genes for main functions of the cyanobacterial cell, i.e. PSI, PSII, phycobilisomes, and synthesis of compatible solutes, such as ion homeostasis, distinct kinetic patterns were found. While most of the genes for basal physiological functions were transiently repressed during the 1st h after the onset of salt stress, genes for proteins specifically related to salt acclimation were activated. This gene expression pattern reflects well the changes in main physiological processes in salt-stressed cells, i.e. transient inhibition of photosynthesis and pigment synthesis as well as immediate activation of synthesis of compatible solutes. The results clearly document that following the kinetics of genome-wide expression, profiling can be used to envisage physiological changes in the cyanobacterial cell after certain changes in growth conditions.
Molecular and Functional Characterization of a Family of Amino Acid Transporters from Arabidopsis
Authors: Su Yan-Hua , Frommer Wolf B. , Ludewig Uwe
Published: October 2004

More than 50 distinct amino acid transporter genes have been identified in the genome of Arabidopsis, indicating that transport of amino acids across membranes is a highly complex feature in plants. Based on sequence similarity, these transporters can be divided into two major superfamilies: the amino acid transporter family and the amino acid polyamine choline transporter family. Currently, mainly transporters of the amino acid transporter family have been characterized. Here, a molecular and functional characterization of amino acid polyamine choline transporters is presented, namely the cationic amino acid transporter (CAT) subfamily. CAT5 functions as a high-affinity, basic amino acid transporter at the plasma membrane. Uptake of toxic amino acid analogs implies that neutral or acidic amino acids are preferentially transported by CAT3, CAT6, and CAT8. The expression profiles suggest that CAT5 may function in reuptake of leaking amino acids at the leaf margin, while CAT8 is expressed in young and rapidly dividing tissues such as young leaves and root apical meristem. CAT2 is localized to the tonoplast in transformed Arabidopsis protoplasts and thus may encode the long-sought vacuolar amino acid transporter.
Regulation of Sulfate Uptake and Expression of Sulfate Transporter Genes in Brassica oleracea as Affected by Atmospheric H2S and Pedospheric Sulfate Nutrition
Authors: Buchner Peter , Stuiver C. Elisabeth E. , Westerman Sue , Wirtz Markus , Hell Rüdiger , Hawkesford Malcolm J. , De Kok Luit J.
Published: October 2004

Demand-driven signaling will contribute to regulation of sulfur acquisition and distribution within the plant. To investigate the regulatory mechanisms pedospheric sulfate and atmospheric H2S supply were manipulated in Brassica oleracea. Sulfate deprivation of B. oleracea seedlings induced a rapid increase of the sulfate uptake capacity by the roots, accompanied by an increased expression of genes encoding specific sulfate transporters in roots and other plant parts. More prolonged sulfate deprivation resulted in an altered shoot-root partitioning of biomass in favor of the root. B. oleracea was able to utilize atmospheric H2S as S-source; however, root proliferation and increased sulfate transporter expression occurred as in S-deficient plants. It was evident that in B. oleracea there was a poor shoot to root signaling for the regulation of sulfate uptake and expression of the sulfate transporters. cDNAs corresponding to 12 different sulfate transporter genes representing the complete gene family were isolated from Brassica napus and B. oleracea species. The sequence analysis classified the Brassica sulfate transporter genes into four different groups. The expression of the different sulfate transporters showed a complex pattern of tissue specificity and regulation by sulfur nutritional status. The sulfate transporter genes of Groups 1, 2, and 4 were induced or up-regulated under sulfate deprivation, although the expression of Group 3 sulfate transporters was not affected by the sulfate status. The significance of sulfate, thiols, and O-acetylserine as possible signal compounds in the regulation of the sulfate uptake and expression of the transporter genes is evaluated.
Overexpression ofConstitutive Differential Growth 1Gene, Which Encodes a RLCKVII-Subfamily Protein Kinase, Causes Abnormal Differential and Elongation Growth after Organ Differentiation in Arabidopsis
Authors: Muto Hideki , Yabe Naoto , Asami Tadao , Hasunuma Koji , Yamamoto Kotaro T.
Published: October 2004

To better understand genetic regulation of differential growth of plant organs, a dominant and semidwarf mutant, constitutive differential growth 1-Dominant (cdg1-D), was isolated utilizing the technique of activation tagging. cdg1-D showed pleiotropic phenotype including dwarfism, exaggerated leaf epinasty, and twisted or spiral growth in hypocotyl, inflorescence stem, and petiole. Hypocotyls of cdg1-D were longer than those of wild type under light conditions. The phenotype was caused by activation tagging of CDG1 gene that encodes a receptor-like cytoplasmic kinase of RLCKVII subfamily. When treated with high concentrations of brassinolide, light-grown wild-type seedlings showed long hypocotyls and strong leaf epinasty as observed in cdg1-D seedlings. Treatment of cdg1-D with brassinazole, a specific inhibitor of brassinosteroid (BR) biosynthesis, did not rescue the mutant phenotype. Gene expression of CONSTITUTIVE PHOTOMORPHOGENESIS AND DWARFISM involved in BR biosynthesis and phyB ACTIVATION-TAGGED SUPPRESSOR1 that inactivates BR was repressed and induced, respectively, in cdg1-D plants, suggesting constitutive activation of BR signaling in the mutant. CDG1 was expressed at a very low level in all the organs of the wild type tested. We isolated two independent intragenic suppressors of cdg1-D. However, they showed normal morphology and responded to BR in a similar manner to wild type. Taken together, CDG1 gene may interfere with signal transduction of BR when overexpressed, but is not an essential factor for it in the wild type.
Isolation and Characterization of an Arabidopsis Mutant That Overaccumulates O-Acetyl-l-Ser
Authors: Ohkama-Ohtsu Naoko , Kasajima Ichiro , Fujiwara Toru , Naito Satoshi
Published: October 2004

O-Acetyl-l-Ser (OAS) is a positive regulator for the expression of sulfur (S) deficiency-inducible genes. In this study, through the isolation and analysis of Arabidopsis mutants exhibiting altered expression of S-responsive genes, we identified a thiol reductase as a regulator of the OAS levels. Ethyl methanesulfonate-mutagenized M2 seeds of transgenic Arabidopsis NOB7 carrying a chimeric S-responsive promoter driving the green fluorescent protein gene were screened for mutants with altered levels of green fluorescence compared to parental NOB7 line. One of the lines exhibited elevated levels of green fluorescence and mRNA accumulation of several endogenous S-responsive genes and carried a single recessive mutation responsible for the phenotype. OAS concentration in the rosette leaves of the mutant was about five times higher than that of wild-type plants. Based upon the high OAS levels, the mutant was named osh1-1 (OAS high accumulation). The OSH1 locus was mapped to a 30-kb region in chromosome V. DNA sequence analysis revealed no base change in this region; however, a demethylated C residue was found in the first exon of At5g01580. At5g01580 mRNA accumulation was higher in osh1-1 than in wild type, while transcript levels of other genes in the mapped region were not significantly altered in osh1-1. A line of transgenic plants overexpressing At5g01580 had elevated levels of endogenous S-responsive genes. These results suggest that elevated expression of At5g01580 is the cause of osh1 phenotype. Based on sequence similarity to animal thiol reductases, At5g01580 was tested for and exhibited thiol reductase activity. Possible roles of a thiol reductase in OAS metabolism are discussed.
Requirement of the Histidine Kinase Domain for Signal Transduction by the Ethylene Receptor ETR1
Authors: Qu Xiang , Schaller G. Eric
Published: October 2004

In Arabidopsis, ethylene is perceived by a receptor family consisting of five members, one of these being ETR1. The N-terminal half of ETR1 functions as a signal input domain. The C-terminal region of ETR1, consisting of a His kinase domain and a putative receiver domain, is likely to function in signal output. The role of the proposed signal output region in ethylene signaling was examined in planta. For this purpose, the ability of mutant versions of ETR1 to rescue the constitutive ethylene-response phenotype of the etr1-6;etr2-3;ein4-4 triple loss-of-function mutant line was examined. A truncated version of ETR1 that lacks both the His kinase domain and the receiver domain failed to rescue the triple mutant phenotype. A truncated ETR1 receptor that lacks only the receiver domain restored normal growth to the triple mutant in air, but the transgenic seedlings displayed hypersensitivity to low doses of ethylene. A mutation that eliminated His kinase activity had a modest effect upon the ability of the receptor to repress ethylene responses in air. These results demonstrate that the His kinase domain plays a role in the repression of ethylene responses. The potential roles of the receiver domain and His kinase activity in ethylene signaling are discussed.
Characterization of the Silicon Uptake System and Molecular Mapping of the Silicon Transporter Gene in Rice
Authors: Ma Jian Feng , Mitani Namiki , Nagao Sakiko , Konishi Saeko , Tamai Kazunori , Iwashita Takashi , Yano Masahiro
Published: October 2004

Rice (Oryza sativa L. cv Oochikara) is a typical silicon-accumulating plant, but the mechanism responsible for the high silicon uptake by the roots is poorly understood. We characterized the silicon uptake system in rice roots by using a low-silicon rice mutant (lsi1) and wild-type rice. A kinetic study showed that the concentration of silicon in the root symplastic solution increased with increasing silicon concentrations in the external solution but saturated at a higher concentration in both lines. There were no differences in the silicon concentration of the symplastic solution between the wild-type rice and the mutant. The form of soluble silicon in the root, xylem, and leaf identified by 29Si-NMR was also the same in the two lines. However, the concentration of silicon in the xylem sap was much higher in the wild type than in the mutant. These results indicate that at least two transporters are involved in silicon transport from the external solution to the xylem and that the low-silicon rice mutant is defective in loading silicon into xylem rather than silicon uptake from external solution to cortical cells. To map the responsible gene, we performed a bulked segregant analysis by using both microsatellite and expressed sequence tag-based PCR markers. As a result, the gene was mapped to chromosome 2, flanked by microsatellite marker RM5303 and expressed sequence tag-based PCR marker E60168.
The Arabidopsis phenylalanine insensitive growth Mutant Exhibits a Deregulated Amino Acid Metabolism
Authors: Voll Lars M. , Allaire Erin E. , Fiene Gabriele , Weber Andreas P.M.
Published: October 2004

Amino acids and amino acid analogs have been used in numerous genetic screens to isolate mutants deficient in amino acid biosynthetic pathways or in the regulation of amino acid metabolism. Several of these mutants exhibit relaxed feedback control of branched amino acid biosynthetic pathways and are thus resistant to accumulation of pathway end products. For example, feedback-regulated enzymes of the shikimate pathway are anthranilate synthase on the branch leading to Trp and chorismate mutase on the branch leading to Phe and Tyr. A feedback-insensitive mutant of anthranilate synthase α, trp5-1, is resistant to toxic Trp analogs. Mutants resistant to Phe have not previously been reported, and this article describes the isolation of the recessive Arabidopsis Phe insensitive growth mutant pig1-1 by a forward genetic screen. pig1-1 was not only tolerant to Phe, Tyr, and Trp, but also to other, not biosynthetically related amino acids. Amino acid contents in pig1-1 were significantly elevated with respect to wild-type controls but, in contrast to the wild type, dramatically decreased when plants were supplemented with 2 mm Phe. Protein contents were similar in the mutant and the wild type at all tested conditions. Phe catabolism was similar to the wild type in pig1-1 roots but was significantly increased in pig1-1 shoots. Phenylalanine uptake into the root, its root-to-shoot translocation, and Phe and phenylpropanoid contents were unaltered in pig1-1, indicating that pig1-1 is not affected in amino acid translocation or the shikimate pathway. Instead, the response of pig1-1 toward amino acid feeding indicates that amino acid metabolism is generally deregulated in pig1-1.