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Accelerated deamination of cytosine residues in UV-induced cyclobutane pyrimidine dimers leads to CC-->TT transitions.

The rate of UV-induced deamination of cytosine to uracil at a specific site in double-stranded (ds) DNA was monitored using a genetic reversion assay. M13mp2C141 ds DNA was exposed to 160 J/m2 UV (254 nm), incubated at 37 degrees C, pH 7.4, for various time intervals to allow for deamination, and treated with Escherichia coli photolyase in the presence of 365 nm light to reverse cyclobutane-type pyrimidine dimers. Upon transfection into uracil-glycosylase deficient (ung-) E. coli cells, the mutation (i.e., reversion) frequencies in the CCCC target sequence increased greatly with post-UV time of incubation at 37 degrees C, nearly doubling every day that the DNA had been held at 37 degrees C. After 8 days, the reversion frequencies had increased by two orders of magnitude upon transfection into ung- cells, relative to isogenic ung+ cells, indicating that most of the mutations arising in UV/photolyase-treated ds DNA were C-->T mutations mediated by a uracil intermediate. Sequencing of the revertants revealed that all mutations were single C-->T or tandem double CC-->TT mutations. An increasing percentage of tandem double CC-->TT mutations was found with longer post-UV incubation times, yet none occurred if the post-UV delay time step was omitted before photoreversal. After a 4-day delay between UV and photoreversal at 37 degrees C, greater than 84% of the total revertants had tandem double CC-->TT mutations. Thus, the generation of a tandem double mutation is a time-dependent process that arises in DNA after the initial UV exposure. The rate of appearance (with a pseudo-first-order rate constant ca. 10(-6) s-1) of tandem double mutations during incubation of UV-irradiated DNA is inconsistent with two random, independently occurring mutational events and suggests a concerted deamination of both residues in a tandem cytosine pyrimidine (C < > C) dimer. Considering that deamination in a C < > C dimer occurred here with a half-life of ca. 5 days, in contrast to the measured half-life of ca. 20,000 years for spontaneous (non-UV-treated) cytosine deamination for the same target, these studies show that the formation of pyrimidine dimers in DNA increases the rate of deamination by six orders of magnitude, leading to the accelerated formation of single C-->T and tandem double CC-->TT mutations.

Bacteriophage M13↗

A pectinmethylesterase gene associated with a heat-stable extract from citrus.

A putative thermostable pectinmethylesterase (TSPME) protein of 36 kDa was isolated from heat-treated citrus finisher pulp. After purification and partial sequencing of the protein, a reverse genetic approach was used to obtain the complete genomic sequence of a new pectinmethylesterase (PME) gene, CsPME4, from Citrus sinensis (L.) Osb. cv. Valencia. The CsPME4 gene contained two exons of 1203 and 690 bp interrupted by a single positionally conserved intron of 1230 bp. A full-length CsPME4 cDNA clone amplified from Valencia orange juice vesicles shared 98% identity with the genomic clone. The encoded protein of the full-length CsPME4 cDNA shared 66 and 39% amino acid identity with the full-length encoded proteins of the citrus PME, CsPME1, and CsPME3, respectively, whereas the predicted mature protein of CsPME4 shared 80 and 61% identity with the predicted mature proteins of CsPME1 and CsPME3, respectively. Southern analysis demonstrated that CsPME4 was present in at least two copies in the Valencia orange genome. Northern analysis revealed that CsPME4 mRNA was accumulated mainly in young and developing tissues of Valencia orange. Several approaches to express recombinant CsPME4 in different systems failed to obtain active protein. Further research will be necessary to successfully express the putative TSPME gene CsPME4 for biochemical characterization.

Amino Acid Sequence↗

Molecular characterization of myosin V from Drosophila melanogaster.

Recent studies have revealed unconventional myosin V to be an important actin-based molecular motor involved in vesicular movement. In this paper we report the molecular characterization of the Drosophila myosin V, identified by reverse genetics. The gene encodes a 1792-residue, 207 kDa heavy chain polypeptide which possesses a typical head or motor domain of 771 residues, a region of six IQ motifs (139 residues) which serve as potential calmodulin/light chain binding sites at the head/tail junction, and a tail domain of 882 residues containing sequences of putative alpha-helical coiled-coils required for dimerization of the molecule and sequences of non-helical structure at the C-terminal end. Based on Southern blot analyses and chromosomal localization, evidence is presented for a single Drosophila myosin V gene. RNA analyses revealed a doublet of transcripts of about 6 kb, expressed throughout the lifetime of a fly but particularly abundant in the early stages of embryonic development (maternally contributed), in the ectodermic tissue of the hindgut starting at stage 16, and in the adult head. These results suggest that myosin V may be involved in processes required in a variety of cell types in Drosophila. We have also mapped the Drosophila myosin V locus to chromosome 2 at the position 43C-D, and we are currently searching for known mutations in this region. Finally, phylogenetic analysis of the head domain reveals that Drosophila myosin V is more closely related to mammalian myosin Va and Vb than to other invertebrate class-V myosins; nevertheless, it is not significantly more related to myosin Va than to myosin Vb. While vertebrates would need two different myosin V isoforms to accomplish specific functions, we speculate that Drosophila myosin V might provide the equivalent functions by itself.

Amino Acid Sequence↗

Excision of Ds1 from the genome of maize streak virus in response to different transposase-encoding genes.

We have previously established a reverse genetic system for studying excision of the transposable element Ds1 in maize plants. Ds1 carried by the genome of maize streak virus (MSV) is introduced into maize plants by agroinfection. Excision of Ds1 from the MSV genome depends on the presence of an active Ac element in the recipient maize plants. With the purpose of exploiting MSV-Ds1 as vector for maize transformation, we studied different genes encoding the transposase (TPase) for their efficiency of activating Ds1 excision. These genes were inserted in the same T-DNA carrying MSV-Ds1 and introduced into maize plants by Agrobacterium-mediated transformation. We showed that the wild-type TPase transcribed by the 2' promoter produced much higher efficiency of Ds1 excision than that transcribed by the Ac promoter. In contrast to what had been observed in tobacco and petunia, the truncated TPase (103-807) lacking the amino-terminal 102 amino acids gave a much more reduced Ds1 excision efficiency than the wild-type TPase when both genes were transcribed by the 2' promoter.

DNA Transposable Elements↗

Structure and functional analysis of the 26S proteasome subunits from plants.

As initial steps to define how the 26S proteasome degrades ubiquitinated proteins in plants, we have characterized many of the subunits that comprise the proteolytic complex from Arabidopsis thaliana. A set of 23 Arabidopsis genes encoding the full complement of core particle (CP) subunits and a collection encoding 12 out of 18 known eukaryotic regulatory particle (RP) subunits, including six AAA-ATPase subunits, were identified. Several of these 26S proteasome genes could complement yeast strains missing the corresponding orthologs. Using this ability of plant subunits to functionally replace yeast counterparts, a parallel structure/function analysis was performed with the RP subunit RPN 10/MCB1, a putative receptor for ubiquitin conjugates. RPN10 is not essential for yeast viability but is required for amino acid analog tolerance and degradation of proteins via the ubiquitin-fusion degradation pathway, a subpathway within the ubiquitin system. Surprisingly, we found that the C-terminal motif required for conjugate recognition by RPN10 is not essential for in vivo functions. Instead, a domain near the N-terminus is required. We have begun to exploit the moss Physcomitrella patens as a model to characterize the plant 26S proteasome using reverse genetics. By homologous recombination, we have successfully disrupted the RPN10 gene. Unlike yeast rpn10delta strains which grow normally, Physcomitrella rpn10delta strains are developmentally arrested, being unable to initiate gametophorogenesis. Further analysis of these mutants revealed that RPN10 is likely required for a developmental program triggered by plant hormones.

Arabidopsis↗

A transgenic perspective on plant functional genomics.

Transgenic crops are very much in the news due to the increasing public debate on their acceptance. In the scientific community though, transgenic plants are proving to be powerful tools to study various aspects of plant sciences. The emerging scientific revolution sparked by genomics based technologies is producing enormous amounts of DNA sequence information that, together with plant transformation methodology, is opening up new experimental opportunities for functional genomics analysis. An overview is provided here on the use of transgenic technology for the functional analysis of plant genes in model plants and a link made to their utilization in transgenic crops. In transgenic plants, insertional mutagenesis using heterologous maize transposons or Agrobacterium mediated T-DNA insertions, have been valuable tools for the identification and isolation of genes that display a mutant phenotype. To discover functions of genes that do not display phenotypes when mutated, insertion sequences have been engineered to monitor or change the expression pattern of adjacent genes. These gene detector insertions can detect adjacent promoters, enhancers or gene exons and precisely reflect the expression pattern of the tagged gene. Activation tag insertions can mis-express the adjacent gene and confer dominant phenotypes that help bridge the phenotype gap. Employment of various forms of gene silencing technology broadens the scope of recovering knockout phenotypes for genes with redundant function. All these transgenic strategies describing gene-phenotype relationships can be addressed by high throughput reverse genetics methods that will help provide functions to the genes discovered by genome sequencing. The gene functions discovered by insertional mutagenesis and silencing strategies along with expression pattern analysis will provide an integrated functional genomics perspective and offer unique applications in transgenic crops.

Crops, Agricultural↗

The use of functional genomics in C. elegans for studying human development and disease.

The 100 Mb Caenorhabditis elegans genome sequence is the first animal genome to be sequenced in its entirety. Many reverse-genetics tools have been developed to mine the genome sequence and to facilitate the jump between the identification of a gene sequence and the understanding of its function. Here we discuss how C. elegans can contribute to understanding of the function of genes involved in human development and disease.

Animals↗

Early and multiple Ac transpositions in rice suitable for efficient insertional mutagenesis.

A GFP excision assay was developed to monitor the excision of Ac introduced into rice by Agrobacterium-mediated transformation. The presence of a strong double enhancer element of the CaMV 35S promoter adjacent to the Ac promoter induced very early excision, directly after transformation into the plant cell, exemplified by the absence of Ac in the T-DNA loci. Excision fingerprint analysis and characterization of transposition events from related regenerants revealed an inverse correlation between the number of excision events and transposed Ac copies, with single early excisions after transformation generating Ac amplification. New transpositions were generated at a frequency of 15-50% in different lines, yielding genotypes bearing multiple insertions, many of which were inherited in the progeny. The sequence of DNA flanking Ac in three representative lines provided a database of insertion tagged sites suitable for the identification of mutants of sequenced genes that can be examined for phenotypes in a reverse genetics strategy to elucidate gene function. Remarkably, two-thirds of Ac tagged sites showing homology to sequences in public databases were in predicted genes. A clear preference of transposon insertions in genes that are either predicted by protein coding capacity or by similarity to ESTs suggests that the efficiency of recovering knockout mutants of genes could be about three times higher than random. Linked Ac transposition, suitable for targeted tagging, was documented by segregation analysis of a crippled Ac element and by recovery of a set of six insertions in a contiguous sequence of 70 kb from chromosome 6 of rice.

Base Sequence↗

Identification of Mutator insertional mutants of starch-branching enzyme 1 (sbe1) in Zea mays L.

Starch-branching enzymes (SBE) alter starch structure by breaking an alpha-1,4 linkage and attaching the reducing end of the new chain to a glucan chain by an alpha 1,6 bond. In maize, three isoforms of SBE have been identified. In order to examine the function of the SBEI isoform, a reverse-genetics PCR-based screen was used to identify a mutant line segregating for a Mutator transposon within Sbe1. Compared to wild-type controls, Sbe1 transcripts accumulate at extremely low levels in leaves of the homozygous mutant. Antibodies failed to detect SBEI in leaf tissue of mutants or wild-type controls. In contrast, the level of SBEI in endosperm is undetectable in homozygous mutants while easily detected in wild-type controls. Starches extracted from mutant leaves and endosperm have structures indistinguishable from starches of wild-type controls as determined by size-exclusion chromatography (SEC) of intact starch and high-performance SEC of debranched starch. To investigate the possibility of compensation for the lack of SBEI by expression of the homologous sequence reported by Kim etal. (1998), agenomic fragment (Sbe1b) of this sequence was cloned. Northern hybridizations of mutant leaf, root, tassel, endosperm and embryo tissues with non-specific Sbelb probes failed to reveal expression of the homologous sequence. These results suggest that the homologous sequence is not compensating for a lack of SBEI in sbe1::Mu mutants. Further study of this sbel mutation in the presence of other genetic mutations may help to understand the role of SBEI in determining starch structure in leaves and endosperm.

1,4-alpha-Glucan Branching Enzyme↗

Expression of the high capacity calcium-binding domain of calreticulin increases bioavailable calcium stores in plants.

Modulation of cytosolic calcium levels in both plants and animals is achieved by a system of Ca2+-transport and storage pathways that include Ca2+ buffering proteins in the lumen of intracellular compartments. To date, most research has focused on the role of transporters in regulating cytosolic calcium. We used a reverse genetics approach to modulate calcium stores in the lumen of the endoplasmic reticulum. Our goals were two-fold: to use the low affinity, high capacity Ca2+ binding characteristics of the C-domain of calreticulin to selectively increase Ca2+ storage in the endoplasmic reticulum, and to determine if those alterations affected plant physiological responses to stress. The C-domain of calreticulin is a highly acidic region that binds 20-50 moles of Ca2+ per mole of protein and has been shown to be the major site of Ca2+ storage within the endoplasmic reticulum of plant cells. A 377-bp fragment encoding the C-domain and ER retention signal from the maize calreticulin gene was fused to a gene for the green fluorescent protein and expressed in Arabidopsis under the control of a heat shock promoter. Following induction on normal medium, the C-domain transformants showed delayed loss of chlorophyll after transfer to calcium depleted medium when compared to seedlings transformed with green fluorescent protein alone. Total calcium measurements showed a 9-35% increase for induced C-domain transformants compared to controls. The data suggest that ectopic expression of the calreticulin C-domain increases Ca2+ stores, and that this Ca2+ reserve can be used by the plant in times of stress.

Agrobacterium tumefaciens↗

A PCR-based assay to detect hAT-like transposon sequences in plants.

Despite their potential as endogenous tools for forward and reverse genetics, members of the hobo, Ac, Tam3 (or hAT) superfamily of transposable elements have been characterized in but a limited number of plant species. To expedite their isolation, we developed a PCR-based assay for the detection of hAT-like transposon sequences in plants which was applied to isolate and initially characterize such sequences from Petunia hybrida, Phaseolus vulgaris, Bambusa vulgaris, Brassica napus and Rhododendron simsii.

DNA Transposable Elements↗

Approach for functional analysis of glycan using RNA interference.

The elucidation of the biological role of glycan is one of the most important issues to be resolved following the genome project. RNA interference is becoming an efficient reverse genetic tool for studying gene function in model organisms, including C.elegans and Drosophila melanogaster. Our molecular evolutionary study has shown that a prototype of glycosyltransferases, which synthesize a variety of glycan structures in the Golgi apparatus, was conserved between mammals and Drosophila. For analyses of the basic physiological functions of glycans, we established the Drosophila inducible RNAi knockdown system and applied it to one glycosyltransferase and one transporter, proteoglycan UDP-galactose: beta-xylose beta1,4galactosyltransferase I and the PAPS-transporter, respectively. If on the silencing of each gene induced ubiquitously under the control of a cytoplasmic actin promoter, the RNAi knockdown fly died, then the protein was indispensable for life. The expression of the target gene was disrupted specifically and the degree of interference was well correlated with the phenotype. The inducible RNAi knockdown fly obtained using the GAL4-UAS system will pave the way for the functional analysis of glycans.

Actins↗

Neuron-specific gene manipulations to transparent zebrafish embryos.

To investigate the molecular basis of neural network formation, we introduced a novel double-cassette vector approach for visualizing and manipulating neuronal development in living zebrafish embryos. Two genes are physically linked in the double-cassette vector system, which ensures co-expression of an effector-protein and an EGFP-reporter in the same neuron. By generating transgenic enhanced green fluorescent protein (EGFP) expressing zebrafish lines, we first established that EGFP under control of either the olfactory marker protein (OMP) gene promoter or the nicotinic acetylcholine receptor beta3 (nAChRbeta3) gene promoter, directed strong EGFP expression to the olfactory sensory neurons and the retinal ganglion cells (RGCs), respectively. These transgenic lines allowed the visualization of the development of the entire olfactory sensory neurons and RGCs in vivo. By injection of vectors with EGFP under control of either the OMP or the nAChRbeta3 gene promoter, we followed the development of individual olfactory sensory neurons and RGCs. The double-cassette expression vector strategy enabled us to clarify the roles of protein kinase A (PKA) and glycogen synthase kinase-3beta (GSK-3beta) in the development of olfactory sensory neurons and RGCs. The combination of visualization and neuron-specific gene manipulation provides a powerful reverse genetic in vivo approach for the study of genes of interest in neural differentiation, axonal pathfinding, and synaptogenesis.

Animals↗

The elongation defective1 mutant of Arabidopsis is impaired in the gene encoding a serine-rich secreted protein.

Coordinated cell growth and differentiation is crucial for the development of higher plants. Using the elongation defective 1-1 (eld1-1) mutant, we cloned the ELD1 gene, which encodes a serine-rich protein. Genes homologous to ELD1 can be found in plants, including Arabidopsis, rice, and tobacco, but not in other organisms. Using reverse genetics, we identified a new allele, eld1-2, which is phenotypically indistinguishable from eld1-1, but does not produce a detectable ELD1 transcript. The ELD1 gene sequence is the same as that of the KOBITO1 sequence. However, the kob1 mutants display weak phenotype relative to the two eld1 mutants, which are likely null alleles. KOB1 was reported to be a membrane protein involved in cellulose synthesis. However, based on ELD1-GFP localization in plasmolyzed cells, we found that ELD1 is localized to the cell wall/extracellular matrix, rather than the membrane. Thus, ELD1/KOB1 is a secreted protein involved in promoting cell growth. To investigate the relationship between ELD1 and Arabidopsis genes with high sequence similarity, we analyzed the possible subcellular location of their proteins as well as their amino acid sequence. The ELD1-related proteins in Arabidopsis were predicted to be localized to subcellular compartments different from that of ELD1. Thus, ELD1 is likely to be functionally distinct from related Arabidopsis genes. These results suggest that ELD1 is a single-copy gene which belongs to a small family of plant-specific genes with diverse function.

Alleles↗

The X-linked chronic granulomatous disease gene codes for the beta-chain of cytochrome b-245.

Chronic granulomatous disease (CGD) is a rare inherited disorder associated with a profound predisposition to infection due to the lack of a microbicidal oxidase system in the phagocytes of these patients. This syndrome is most commonly inherited through a defect on the X chromosome and the only clearly defined component of the oxidase system, the very unusual cytochrome b (b-245), has been shown to be missing from the cells of these patients. This cytochrome is a heterodimer composed of an alpha-chain of relative molecular mass (Mr) 23,000 (23K) and a 76-92K beta-chain; neither are detectable in neutrophils from X-linked CGD subjects. The defective X-CGD gene has recently been cloned by 'reverse genetics' but the protein predicted from the proposed complementary DNA sequence was not identified. We have purified the beta-chain of the cytochrome and sequenced 43 amino acids from the N terminus. Almost complete homology was obtained between this sequence and that of the complementary nucleotides 19-147 of the sequence of the X-CGD gene, originally designated as a non-coding region.

Amino Acid Sequence↗

Cloning of a gene that is rearranged in patients with choroideraemia.

Choroideraemia (tapetochoroidal dystrophy, TCD), a common form of X-linked blindness, is characterized by progressive dystrophy of the choroid, retinal pigment epithelium and retina. Previous studies have assigned the TCD gene to a small segment of the Xq21 band. By making use of reverse genetics strategies we have isolated eight overlapping complementary DNA clones from the same chromosomal region. The corresponding gene is expressed in retina, choroid and retinal pigment epithelium. The cDNAs encompass an open reading frame of 948 base pairs that is structurally altered in eight TCD patients with deletions, and in a female patient with a balanced translocation involving Xq21. These findings provide strong evidence that we have cloned the gene underlying choroideraemia. Elucidation of its function should provide new insights into the molecular mechanisms responsible for this disorder and other hereditary retinopathies.

Amino Acid Sequence↗

Targeted screening for induced mutations.

With the accumulation of large-scale sequence data, emphasis in genomics has shifted from determining gene structure to testing gene function, and this relies on reverse genetic methodology. Here we explore the feasibility of screening for chemically induced mutations in target sequences in Arabidopsis thaliana. Our TILLING (Targeting Induced Local Lesions IN Genomes) method combines the efficiency of ethyl methanesulfonate (EMS)-induced mutagenesis with the ability of denaturing high-performance liquid chromatography (DHPLC) to detect base pair changes by heteroduplex analysis. Importantly, this method generates a wide range of mutant alleles, is fast and automatable, and is applicable to any organism that can be chemically mutagenized.

Alleles↗

Enhanced virulence of influenza A viruses with the haemagglutinin of the 1918 pandemic virus.

The 'Spanish' influenza pandemic of 1918-19 was the most devastating outbreak of infectious disease in recorded history. At least 20 million people died from their illness, which was characterized by an unusually severe and rapid clinical course. The complete sequencing of several genes of the 1918 influenza virus has made it possible to study the functions of the proteins encoded by these genes in viruses generated by reverse genetics, a technique that permits the generation of infectious viruses entirely from cloned complementary DNA. Thus, to identify properties of the 1918 pandemic influenza A strain that might be related to its extraordinary virulence, viruses were produced containing the viral haemagglutinin (HA) and neuraminidase (NA) genes of the 1918 strain. The HA of this strain supports the pathogenicity of a mouse-adapted virus in this animal. Here we demonstrate that the HA of the 1918 virus confers enhanced pathogenicity in mice to recent human viruses that are otherwise non-pathogenic in this host. Moreover, these highly virulent recombinant viruses expressing the 1918 viral HA could infect the entire lung and induce high levels of macrophage-derived chemokines and cytokines, which resulted in infiltration of inflammatory cells and severe haemorrhage, hallmarks of the illness produced during the original pandemic.

Adolescent↗