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E Pichersky

Publications and source records attributed to E Pichersky.

At least 55 records · Page 3Linked to original sources
PubMed1992

Sequence of the fourth and fifth Photosystem II type I chlorophyll a/b-binding protein genes of Arabidopsis thaliana and evidence for the presence of a full complement of the extended CAB gene family.

A second locus (Lhb1B) encoding Photosystem II Type I chlorophyll a/b-binding (CAB) polypeptides was identified in Arabidopsis thaliana. This locus carries two genes in an inverted orientation. The predicted sequences of the polypeptides encoded by these two genes show substantial divergence in their amino termini relative to each other and to the proteins encoded by the three Lhb1 CAB genes previously characterized [10], but little divergence within the predicted primary structure of the mature protein. DNA probes derived from seven additional types of tomato CAB genes, encoding chlorophyll a/b-binding polypeptides of several antenna systems of the photosynthetic apparatus, were tested against A. thaliana. Each of these hybridized in Southern blots to unique DNA fragment(s), demonstrating the existence of each of these different types of CAB genes in the genome of A. thaliana. The number of genes encoding each CAB type in A. thaliana was estimated to be similar to that of tomato.

Base Sequence↗
PubMed1991

Nucleotide sequence and chromosomal location of Cab11 and Cab12, the genes for the fourth polypeptide of the photosystem I light-harvesting antenna (LHCI).

Tryptic peptide sequences from the 22 kDa polypeptide of tomato LHCI were used to construct a probe for gene cloning. The two genes cloned, cab11 and cab12, encode proteins of 251 and 250 residues that are 88% identical in overall amino acid sequence and 93% identical in the deduced mature protein. Each gene is present in a single copy per haploid genome; cab11 on chromosome 3 and cab12 on chromosome 6, and each has 2 introns located in similar positions to introns in other members of the Chl a/b-binding (CAB) protein gene family. Comparison of the amino acid sequences of LHCI, LHCII, CP29 and CP24 polypeptides confirms that all CABs share two regions of very high similarity which include the first and third transmembrane helices and the stroma-exposed sequences preceding them. However, near the N-terminus and between the conserved regions, the LHCI polypeptides have sequence motifs which appear to be PSI-specific.

Amino Acid Sequence↗
PubMed1991

Isolation and characterization of tomato cDNA and genomic clones encoding the ubiquitin gene ubi3.

We report here the isolation and nucleotide sequence of tomato cDNA and genomic clones encoding a ubiquitin extension protein homologous to the yeast gene ubi3. Sites similar to upstream activating sites commonly found in the promoters of yeast ribosomal genes were observed in the tomato promoter. The tomato ubi3 promoter also contained elements found in the rbcS promoter from pea. The transcription initiation site was determined to occur 66 bp upstream of the initiating Met. RFLP mapping revealed that the gene was located on chromosome 1, 23 cM from marker TG301. A ubi3 gene-specific probe hybridized to a single 800 nt transcript. Expression was reduced in heat-shocked plants and plants kept in the dark. Expression was highest in young leaves and immature green fruit and lowest in mature leaves and petals. We isolated the original cDNA clone using an antibody prepared against chloroplast polypeptides. Immunological studies did not detect ubiquitin or ubiquitin extension proteins in the chloroplast. However, higher-molecular-weight chloroplast proteins were detected with ubiquitin antisera suggesting that ubiquitin conjugates are transported into the chloroplast.

Amino Acid Sequence↗
PubMed1991

Chlorophyll a/b binding (CAB) polypeptides of CP29, the internal chlorophyll a/b complex of PSII: characterization of the tomato gene encoding the 26 kDa (type I) polypeptide, and evidence for a second CP29 polypeptide.

CP29, the core chlorophyll a/b (CAB) antenna complex of Photosystem II (PSII), has two nuclear-encoded polypeptides of approximately 26 and 28 kDa in tomato (Lycopersicon esculentum). Cab9, the gene for the Type I (26 kDa) CP29 polypeptide was cloned by immunoscreening a tomato leaf cDNA library. Its identity was confirmed by sequencing tryptic peptides from the mature protein. Cab9 is a single-copy gene with five introns, the highest number found in a CAB protein. In vitro transcription-translation gave a 31 kDa precursor which was cleaved to about 26 kDa after import into isolated tomato chloroplasts. The Cab9 polypeptide has the two highly conserved regions common to all CAB polypeptides, which define the members of this extended gene family. Outside of the conserved regions, it is only slightly more closely related to other PSII CABs than to PSI CABs. Sequence analysis of tryptic peptides from the Type II (28 kDa) CP29 polypeptide showed that it is also a member of the CAB family and is very similar or identical to the CP29 polypeptide previously isolated from spinach. All members of the CAB family have absolutely conserved His, Gln and Asn residues which could ligate the Mg atoms of the chlorophylls, and a number of conserved Asp. Glu, Lys and Arg residues which could form H-bonds to the polar groups on the porphyrin rings. The two conserved regions comprise the first and third predicted trans-membrane helices and the stroma-exposed segments preceding them.

Amino Acid Sequence↗
PubMed1991

Fragments of plastid DNA in the nuclear genome of tomato: prevalence, chromosomal location, and possible mechanism of integration.

We have undertaken a systematic search for plastid DNA sequences integrated in the tomato nuclear genome, using heterologous probes taken from intervals of a plastid DNA region spanning 58 kb. A total of two short integrates (202 and 141 nucleotides) were isolated and mapped to chromosomes 9 and 5, respectively. The nucleotide sequence of the integrates and that of the flanking regions were determined. The integration sites contain direct repeat elements similar in position (but not in length or sequence) to the direct repeats previously observed with another plastid integrate in the tomato nuclear genome. Based on these results, a model for the process of movement and integration of plastid sequences into the nuclear genome is discussed.

Amino Acid Sequence↗
PubMed1991

Determination of steady-state mRNA levels of individual chlorophyll a/b binding protein genes of the tomato cab gene family.

The steady-state levels of mRNA produced by 14 genes encoding members of the tomato chlorophyll a/b binding protein family were quantified. All genes were found to be expressed in leaf tissue, but the mRNAs accumulated to significantly different levels. The transcripts of cab 1A, cab 1B, cab 3A and cab 3B, encoding the Type I LHC proteins of photosystem II, are abundant, while low levels were measured for mRNAs encoding the Type II LHC II and the LHC I proteins. Sequences from the 5' upstream regions (-400 to translational start) of some cab genes were determined in this study, and a total of 16 tomato cab gene promoters for which sequences are now available were analyzed. Significant sequence conservation was found for those genes which are tandemly linked on the chromosome. However, the level of sequence conservation is different for the different cab subfamilies, e.g. 85% similarity between cab 1A and cab 1D vs. 45% sequence similarity between cab 3A and cab 3C upstream sequences. Characteristic GATA repeats with a conserved spacing were found in 5' upstream sequences of cab 1A-D, cab 3A-C, cab 11 and cab 12. The consensus sequence CCTTATCAT, which is believed to mediate light responsiveness, was found at different locations in the upstream sequences of cab 6B, cab 7, cab 8, cab 9, cab 10A, cab 10B and cab 11. In 11 out of 15 genes the transcription initiation site was found to center on the triplet TCA.

Base Sequence↗
PubMed1991

Tomato yellow leaf curl virus: a whitefly-transmitted geminivirus with a single genomic component.

The genome of the tomato yellow leaf curl virus (TYLCV), a Bemisia tabaci-transmitted geminivirus, was cloned. All clones obtained were of one genomic molecule, analogous to DNA A of African cassava mosaic virus. Nucleotide sequence analysis of the TYLCV genome showed that it comprises 2787 nucleotides, encoding six open reading frames, two on the virion strand and four on the complementary strand. All of them have counterparts in other geminiviruses. Dimeric copies of the cloned viral genome were introduced into tomato plants by agroinoculation. Severe yellow leaf curl disease symptoms developed in all of them. Effective whitefly-mediated transmission of the virus from agroinoculated plants to test plants demonstrated that the cloned molecule carries all the information needed for virus replication, systemic infection, and transfer by whiteflies. Restriction and hybridization analyses of viral DNA forms in infected plants and viruliferous whiteflies did not support the presupposed existence of a second genomic component. This is the first report of a whitefly-transmitted geminivirus that possesses a single genomic molecule.

Animals↗
PubMed1991

Chlorophyll a/b-binding proteins: an extended family.

A large proportion of the chlorophyll in a plant is engaged in harvesting light energy and transferring it to the photochemical reaction centres. These 'antenna' chlorophylls are non-covalently bound to specific proteins to form chlorophyll-protein complexes. The chlorophyll a/b-binding (CAB) polypeptides are encoded by an extended family of nuclear genes. It has recently been discovered that other proteins not known to bind chlorophyll, the early light-inducible proteins (ELIPs), are also related and could be considered part of this family. We suggest that the latter proteins may be involved in pigment biosynthesis or in assembly of the thylakoid membrane.

Chlorophyll↗
PubMed1991

Characterization of Cytoplasmic and Nuclear Mutations Affecting Chlorophyll and Chlorophyll-Binding Proteins during Senescence in Soybean.

Soybean plants (Glycine max [L.] Merr. cv Clark) carrying nuclear and cytoplasmic "stay-green" mutations, which affect senescence, were examined. Normally, the levels of chlorophyll (Chl) a and b decline during seedfill and the Chl a/b ratio decreases during late pod development in cv Clark. Plants homozygous for both the d(1) and d(2) recessive alleles, at two different nuclear loci, respectively, retained most (64%) of their Chl a and b and exhibited no change in their Chl a/b ratio. Combination of G (a dominant nuclear allele in a third locus causing only the seed coat to stay green during senescence) with d(1)d(2) further inhibited the loss of Chl in the leaf. Whereas the thylakoid proteins seem to be degraded in normal Clark leaves during late pod development, they were not substantially diminished in d(1)d(2) and Gd(1)d(2) leaves. In plants carrying a cytoplasmic mutation, cytG, Chl declined in parallel with normal cv Clark; however, the cytG leaves had a much higher level of Chl b, and somewhat more Chl a, remaining at abscission, enough to color the leaves green. In cytG, most thylakoid proteins were degraded, but the Chl a/b-binding polypeptides of the light-harvesting complex in photosystem II (LHCII), and their associated Chl a and b molecules, were not. Thus, the combination of d(1) and d(2) causes broad preservation of the thylakoid proteins, whereas cytG appears to selectively preserve LHCII. The cytG mutation may be useful in elucidating the sequence of events involved in the degradation of LHCII proteins and their associated pigments during senescence.

Journal Article↗
PubMed1990

Defective chlorophyll a/b-binding protein genes in the genome of a homosporous fern.

The majority of homosporous ferns have a chromosome number that is severalfold greater than that of diploid seed plants. These fern species have therefore been generally considered to be of polyploid origin. Enzyme electrophoretic investigations have demonstrated, however, that within fern genera, species having the lowest chromosome numbers (n = 27-52) have the number of isozymes typical of diploid seed plants; there is no isozyme evidence for polyploidy of these plants. We have constructed a genomic DNA library from Polystichum munitum (n = 41), a homosporous fern, and have screened the library for sequences homologous to the chlorophyll a/b-binding (CAB) protein genes of higher plants. The majority of the sequences isolated and characterized by nucleotide sequence determination represent defective CAB genes. This result is in contrast to the situation in the genomes of diploid angiosperms, where most, and sometimes all, copies of the CAB gene family represent functional members. Several hypotheses could explain the existence of multiple defective CAB genes in P. munitum. (i) The defective CAB genes are the result of "gene silencing" following polyploidy. (ii) P. munitum has not gone through a polyploidization event, but several, and perhaps the majority, of its CAB genes have mutated to a nonfunctional state (a phenomenon not yet observed in any of the genomes of non-fern plants so far examined). (iii) Some defective CAB genes have been specifically amplified in the genome of P. munitum.

Amino Acid Sequence↗
PubMed1990

Conservation of the regulatory subunit for the Clp ATP-dependent protease in prokaryotes and eukaryotes.

Bacteria, tomatoes, and trypanosomes all contain genes for a large protein with extensive homology to the regulatory subunit, ClpA, of the ATP-dependent protease of Escherichia coli, Clp. All members of the family have between 756 and 926 amino acids and contain two large regions, of 233 and 192 amino acids, each containing consensus sequences for nucleotide binding. Within these regions there is at least 85% similarity between the most distant members of the family. The high degree of similarity among the ClpA-like proteins suggests that Clp-like proteases are likely to be important participants in energy-dependent proteolysis in prokaryotic and eukaryotic cells.

ATP-Dependent Proteases↗
PubMed1990

Analysis of the diurnal expression patterns of the tomato chlorophyll a/b binding protein genes. Influence of light and characterization of the gene family.

Steady-state mRNA levels of the chlorophyll a/b binding (cab) proteins oscillate substantially during a diurnal cycle in tomato leaves. This accumulation pattern is also observed in complete darkness, supporting the hypothesis that the expression of cab genes is at least partially regulated by an endogenous rhythm ("biological clock"). The amplitude of the cab mRNA accumulation is dependent on the duration of illumination and the circadian phase in which light was applied to the tomato plants. These results at the molecular level correlate well with the photoperiodic phenomenon. The characterization of the expression pattern of individual members of the cab gene family was attempted. Distinct primer extension products were detected using specific oligonucleotides homologous to the cab 1, cab 4, cab 5 and cab 8 genes. Based on this analysis the transcription start sites of these genes were determined to be between position -70 and -9 upstream of the ATG codon. During the diurnal cycle the cab 1 and cab 4 genes exhibit the same expression pattern; no transcripts detected at 3 and 6 a.m., maximum mRNA levels were measured at noon and decreasing levels in the afternoon.

Base Sequence↗
PubMed1989

Level of expression of the tomato rbcS-3A gene is modulated by a far upstream promoter element in a developmentally regulated manner.

By Agrobacterium-mediated transformation we have demonstrated that a 1.10-kilobase promoter sequence from the tomato rbcS-3A gene confers light-inducible and organ-specific expression upon fusion to the bacterial chloramphenicol acetyltransferase gene. A biphasic expression profile was obtained by 5' deletion analysis of this promoter, indicating the presence of both positive and negative regulatory elements. A severe reduction in the level of expression was observed when the 5'-terminal 90 base pairs were deleted from the 1.10-kilobase promoter. DNA sequence elements responsible for light inducibility and organ specificity of the gene reside within the -374 base pairs of the proximal part of the promoter and the sequences spanning from -374 to -205 are essential for promoter function. The DNA sequences upstream from -374 modulate the level of expression in leaf tissue; this modulation is under developmental control.

Base Sequence↗
PubMed1988

Chloroplast DNA sequences integrated into an intron of a tomato nuclear gene.

DNA sequences capable of hybridizing with chloroplast DNA have previously been reported to exist in the nuclear genome of higher plants. Here we show that the third intron of the cultivated tomato (Lycopersicon esculentum) nuclear gene Cab-7, which resides on chromosome 10 and which we recently cloned and sequenced, contains two DNA fragments derived from the coding region of the chloroplast gene psbG. The first fragment, 133 bp long, is located at a site 63 bp from the 3' end of the 833 bp intron. The exact sequence of the 11 nucleotides at the 3' end of the inserting chloroplast sequence is also found at the 5' border of the insertion. A small (107 bp) chloroplast DNA fragment is inserted near the middle of the intron, again with the 3' end of the inserting element (6 bp) duplicated at the 5' border of the insertion. The second insert is a subfragment of the first insert, and is most likely directly derived from it. The psbG insertion sequence was found to be present in the Cab-7 gene of all tomato species examined but not in species from related genera (e.g. Solanum, Petunia, Nicotiana), suggesting that the original transposition event (chloroplast to nucleus) occurred relatively recently--since the divergence of the genus Lycopersicon from other genera in the family Solanaceae, but before radiation of species in that genus.

Base Sequence↗