PCR Sampling of disease resistance-like sequences from a disease resistance gene cluster in soybean

Clusters of Resistance-like genes (RLGs) have been identified from a variety of plant species. In soybean, RLG-specific primers and BAC-fingerprinting were used to develop a contig of overlapping BACs for a cluster of RLGs on soybean linkage group J. The resistance genes Rps2 (Phytophthora stem and root rot) and Rmd-c (powdery mildew) and the ineffective nodulation gene Rj2 were previously mapped to this region of linkage group J. PCR hybridization was used to place two TIR/NBD/LRR cDNAs on overlapping BACs from this contig. Both of the cDNAs were present on BAC 34P7. Fingerprinting of this BAC suggested as many as twelve different RLGs were present. Given the high nucleotide identity shared between cDNAs LM6 and MG13 (>90%), direct sequencing of this region would be difficult. More sequence information was needed about the RLGs within this region before sequencing could be undertaken. By comparing the genomic sequences of cDNAs LM6 and MG13 we identified conserved regions from which oligonucleotide primers specific to BAC 34P7 RLGs could be designed. The nine primer pairs spanned the genomic sequence of LM6 and produced overlapping RLG products upon amplification of BAC 34P7. Amplification products from 12 different RLGs were identified. On average, nucleotide identity between RLG sequences was greater than 95%. Examination of RLG sequences also revealed evidence of additions, deletions and duplications within targeted regions of these genes. Using previously mapped cDNAs we were able to quickly and inexpensively access multiple RLGs within a single specific cluster.     

CHARACTERIZATION OF A cDNA ENCODING GLUTAMINE SYNTHETASE FROM THE MARINE DIATOM SKELETONEMA COSTATUM (BACILLARIOPHYCEAE)

A cDNA-encoding glutamine synthetase (GS) was isolated from the marine diatom Skeletonema costatum (Greville) Cleve by PCR amplification. Nucleic acid and deduced amino acid sequences of the diatom GS were greater than 50% identical to GS from green algae and vascular plants, and phylogenetic analysis established the diatom GS as a member of the GSII gene family. The presence of an N-terminus signal sequence, identified on the basis of sequence similarity with other chloroplast-localized proteins from diatoms, suggests that the encoded GS isoenzyme is localized to the chloroplast. The GS mRNA was present in log-phase cells grown with either nitrate or ammonium as the sole added nitrogen source. Results from Southern blot analysis of genomic DNA suggested that the cDNA isolated in this study was either a member of a small, highly conserved gene family or that there was allelic variation within the region examined. Phylogenetic analyses further indicated that genes encoding GS from the diatom and two species of green algae diverged prior to the gene duplication, to the isoenzymes in vascular plants, supporting the hypothesis that GS isoenzymes in diatoms, green algae, and vascular plants arose through independent evolutionary events.     

Feline cytokines TNFα AND IL‐1β: PCR cloning and sequencing of cDNA

Abstract

Using oligonucleotide primers and polymerase chain reaction (PCR), cDNAs for feline cytokines TNFα and IL‐1β were amplified, cloned, and sequenced. The cDNA for PCR amplification was prepared from mRNA derived from lipopolysaccharide (LPS) stimulated feline bone marrow derived macrophages. PCR was performed using sets of oligonucleotide primers designed to specifically amplify cDNAs for IL‐1β or TNFα. PCR fragments were cloned into pGEM 3ZF(‐) or pCR 1000 vectors, sequenced and consensus nucleotide sequences reported.

The cDNA for feline TNFα had a 98.6% match with coding regions of a genomic clone for feline TNFα which was recently reported (McGraw, 1990). The two feline TNFα clones differ by 8 nucleotide base pair (bp) changes which result in 5 amino acid differences in the predicted protein sequence. A search of GenBank and EMBL determined that the feline TNFα cDNA consensus sequence had a 90, 86, 85, 82 and 83 percent overall match with human, porcine, ovine, mouse and goat TNFα cDNAs, respectively. The protein‐coding sequence for feline TNFα from start to stop codon is 702 bp in length and encodes a predicted protein of 233 amino acids with a molecular weight of approximately 25,446 daltons (precursor form of secreted form of TNFα).

The protein‐coding sequence for feline IL‐1β is 804 bp long and encodes a predicted protein of 267 amino acids with a molecular weight of 31,892 daltons (precursor form of secreted IL‐1β). The feline IL‐1β cDNA consensus sequence had an overall match of 79, 76, 77.5 and 77 percent with IL‐1β cDNA from human, bovine, rabbit and murine species, respectively.     

PCR-based immortalization and screening of hierarchical pools of cDNAs.

Starting from sequences of at least 60 bp, PCR-based screening has been developed to recover cDNAs from libraries without the necessity for hybridization or extensive DNA extraction steps. The method maintains the indefinite availability of even scarce cDNA libraries and provides an estimate of the relative abundance of the mRNA species. Isolation of a cDNA clone can be done in less than a week. cDNAs were isolated that were cognate for fragments of expressed sequences and for an exon predicted from genomic sequence.     

The use of direct cDNA selection to rapidly and effectively identify genes in the fungus Aspergillus fumigatus

Aspergillus fumigatus is one of the causes of invasive lung disease in immunocompromised individuals. To rapidly identify genes in this fungus, including potential targets for chemotherapy, diagnostics, and vaccine development, we constructed cDNA libraries. We began with non-normalized libraries, then to improve this approach we constructed a normalized cDNA library using direct cDNA selection. Normalization resulted in a reduction of the frequency of clones with highly expressed genes and an enrichment of underrepresented cDNAs. Expressed sequence tags generated from both the original and the normalized libraries were compared with the genomes of Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Candida albicans, indicating that a large proportion of A. fumigatus genes do not have orthologs in these fungal species. This method allowed the expeditious identification of genes in a fungal pathogen. The same approach can be applied to other human or plant pathogens to rapidly identify genes without the need for genomic sequence information.     

Rapid amplification of genomic ends (RAGE) as a simple method to clone flanking genomic DNA

This report describes the amplification of upstream genomic sequences using the polymerase chain reaction (PCR) based solely on downstream DNA information from a cDNA clone. In this novel and rapid technique, genomic DNA (gDNA) is first incubated with a restriction enzyme that recognizes a site within the 5′ end of a gene, followed by denaturation and polyadenylation of its free 3′ ends with terminal transferase. The modified gDNA is then used as template for PCR using a gene-specific primer complementary to a sequence in the 3′ end of its cDNA and an anchored deoxyoligothymidine primer. A second round of PCR is then performed with a second, nested gene-specific primer and the anchor sequence primer. The resulting PCR product is cloned and its sequence determined. Three independent plant genomic clones were isolated using this method that exhibited complete sequence identity to their cDNAs and to the primers used in the amplification.     

Global amplification of cDNA from limiting amounts of tissue. An improved method for gene cloning and analysis

In this study we present an improved polymerase chain reaction (PCR)-based methodology to generate large amounts of high-quality complementary DNA (cDNA) from small amounts of initial total RNA. Global amplification of cDNA makes it possible to simultaneously clone many cDNAs and to construct directional cDNA libraries from a sequence-abundance-normalized cDNA population, and also permits rapid amplification of cDNA ends (RACE), from a limited amount of starting material. The priming of cDNAs with an adapter oligo-deoxythymidine (oligo-dT) primer and the ligation of a modified oligonucleotide to the 3′ end of single-stranded cDNAs, through the use of T4 RNA ligase, generates known sequences on either end of the cDNA population. This helps in the global amplification of cDNAs and in the sequence-abundance normalization of the cDNA population through the use of PCR. Utilization of a long-range PCR enzyme mix to amplify the cDNA population helps to reduce bias toward the preferential amplification of shorter molecules. Incorporation of restriction sites in the PCR primers allows the amplified cDNAs to be directionally cloned into appropriate cloning vectors to generate cDNA libraries. RACE-PCR done with biotinylated primers and streptavidin-coated para-magnetic particles are used for the efficient isolation of either full-length coding or noncoding strands.     

Construction of Rice cDNA Library and Partial Sequence Analysis of 100 Randomly Selected cDNA

A cDNA library of rice (Oryza sativa ssp. indica cv. "Guangluai 4") etiolated shoot was constructed using Lambda ZAP Ⅱ vector. After analysing the partial sequences of 100 randomly selected clones and database comparison to rice and other plants, 13 % cDNA clones could be identified and 12 % cDNAs had high degree of sequence similarity to partial sequence from rice or other species, whose function is still unknown. The remaining 75% cDNAs showed little or no similarity to genes in the database and might represent novel genes. It demonstrates the suitability of this library for large-scale sequencing from which more information of functional genes will result.     

Isolation and characterization of maize cDNAs encoding a high mobility group protein displaying a HMG-box.

cDNAs encoding a nonhistone chromosomal high mobility group (HMG) protein corresponding to the animal HMG1 family were isolated from a maize cDNA library using an immunoscreening approach. The cDNAs revealed an open reading frame of 471 base pairs together with 413 base pairs of flanking region, in agreement with the size of mRNA detected by Northern analysis of maize endosperm RNA. Like its animal counterparts the 17146 Da maize HMG protein contains a basic aminoterminus and an acidic carboxyterminus. The HMG-box region of this plant HMG protein shows striking sequence similarity to members of the vertebrate HMG1 family. Based on Southern blot hybridization analysis of genomic DNA, the isolated cDNA appears to be derived from a single or low copy gene.     

New perspectives on glutamine synthetase in grasses

Members of the glutamine synthetase (GS) gene family have now been characterized in many crop species such as wheat, rice, and maize. Studies have shown that cytosolic GS isoforms are involved in nitrogen remobilization during leaf senescence and emphasized a role in seed production particularly in small grain crop species. Data from the sequencing of genomes for model crops and expressed sequence tag (EST) libraries from non-model species have strengthened the idea that the cytosolic GS genes are organized in three functionally and phylogenetically conserved subfamilies. Using a bioinformatic approach, the considerable publicly available information on high throughput gene expression was mined to search for genes having patterns of expression similar to GS. Interesting new hypotheses have emerged from searching for co-expressed genes across multiple unfiltered experimental data sets in rice. This approach should inform new experimental designs and studies to explore the regulation of the GS gene family further. It is expected that understanding the regulation of GS under varied climatic conditions will emerge as an important new area considering the results from recent studies that have shown nitrogen assimilation to be critical to plant acclimation to high CO(2) concentrations.