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PubMed2005

What genes make a tree a tree?

Woody growth is evolutionarily ancient, yet has been gained and lost multiple times in plant evolution and is readily enhanced or minimized in eudicot speciation. New molecular genetic and genomic studies in Populus and Arabidopsis that are defining the genes responsible for cambium function and woody growth suggest that the genes regulating woody growth are not unique to woody plants. Surprisingly, key genetic mechanisms originally characterized as regulating the meristematic cells of the shoot apical meristem are also expressed in the vascular cambium during woody growth. This has important implications for the development of Populus as a model species and illustrates why forest trees constitute a contrived group of plants that have more in common with herbaceous relatives than we foresters like to admit.

Biological Evolution↗
PubMed1998

Alfalfa malate dehydrogenase (MDH): molecular cloning and characterization of five different forms reveals a unique nodule-enhanced MDH.

Malate dehydrogenase (MDH) catalyzes the readily reversible reaction of oxaloacetate reversible malate using either NADH or NADPH as a reductant. In plants, the enzyme is important in providing malate for C4 metabolism, pH balance, stomatal and pulvinal movement, respiration, beta-oxidation of fatty acids, and legume root nodule functioning. Due to its diverse roles the enzyme occurs as numerous isozymes in various organelles. While antibodies have been produced and cDNAs characterized for plant mitochondrial, glyoxysomal, and chloroplast forms of MDH, little is known of other forms. Here we report the cloning and characterization of cDNAs encoding five different forms of alfalfa MDH, including a plant cytosolic MDH (cMDH) and a unique novel nodule-enhanced MDH (neMDH). Phylogenetic analyses show that neMDH is related to mitochondrial and glyoxysomal MDHs, but diverge from these forms early in land plant evolution. Four of the five forms could effectively complement an E. coli Mdh- mutant. RNA and protein blots show that neMDH is most highly expressed in effective root nodules. Immunoprecipitation experiments show that antibodies produced to cMDH and neMDH are immunologically distinct and that the neMDH form comprises the major form of total MDH activity and protein in root nodules. Kinetic analysis showed that neMDH has a turnover rate and specificity constant that can account for the extraordinarily high synthesis of malate in nodules.

Amino Acid Sequence↗
PubMed1999

Two types of ftsZ genes isolated from the unicellular primitive red alga Galdieria sulphuraria.

FtsZ plays a crucial role in bacterial cell division, and may be involved in plastid division in eukaryotes. To investigate the evolution of the dividing apparatus from prokaryotes to eukaryotes, the ftsZ genes were isolated from the unicellular primitive red alga Galdieria sulphuraria. Two ftsZ genes (GsftsZ1 and GsftsZ2) were isolated. This suggests that duplication and divergence of the ftsZ gene occurred in an early stage of plant evolution. A comparison of the FtsZs of G. sulphuraria and other organisms shows that FtsZ is highly and universally conserved among prokaryotes, primitive eukaryotic algae, and higher plants. The GsftsZ2 gene seems to contain an intron. Southern hybridization analysis of the G. sulphuraria chromosomes separated by CHEF revealed that each ftsZ gene and its flanking region may be duplicated.

Amino Acid Sequence↗
PubMed1996

Targeting presequence acquisition after mitochondrial gene transfer to the nucleus occurs by duplication of existing targeting signals.

We have cloned a gene for mitochondrial ribosomal protein S11 (RPS11), which is encoded in lower plants by the mitochondrial genome, in higher plants by the nuclear genome, demonstrating genetic information transfer from the mitochondrial genome to the nucleus during flowering plant evolution. The sequence s11-1 encodes an N-terminal extension as well as an organelle-derived RPS11 region. Surprisingly, the N-terminal region has high amino acid sequence similarity with the presequence of the beta-subunit of ATP synthase from plant mitochondria, suggesting a common lineage of the presequences. The deduced N-terminal region of s11-2, a second nuclear-encoded homolog of rps11, shows high sequence similarity with the putative presequence of cytochrome oxidase subunit Vb. The sharing of the N-terminal region together with its 5' flanking untranslated nucleotide sequence in different proteins strongly suggests an involvement of duplication/recombination for targeting signal acquisition after gene migration. A remnant of ancestral rps11 sequence, transcribed and subjected to RNA editing, is found in the mitochondrial genome, indicating that inactivation of mitochondrial rps11 gene expression was initiated at the translational level prior to termination of transcription.

Adenosine Triphosphatases↗
PubMed2003

The evolution of virulence in a plant virus.

The evolution of virulence is a rapidly growing field of research, but few reports deal with the evolution of virulence in natural populations of parasites. We present here an observational and experimental analysis of the evolution of virulence of the plant virus Cucumber mosaic virus (CMV) during an epidemic on tomato in eastern Spain. Three types of CMV isolates were found that caused in tomato plants either a systemic necrosis (N isolates), stunting and a severe reduction of leaf lamina (Y isolates), or stunting and leaf curl (A isolates). These phenotypes were due to the presence of satellite RNAs (satRNAs) necrogenic (in N isolates) or attenuative (in A isolates) of the symptoms caused by CMV without satRNA (Y isolates). For these three types of isolates, parameters of virulence and transmission were estimated experimentally. For virulence the ranking of isolates was N > Y > A, for transmissibility, Y > A > N. The predictions of theoretical models for the evolution of virulence were analyzed with these parameters and compared with observations from the field. A single-infection model predicted adequately the observed long-term evolution of the CMV population to intermediate levels of virulence. A coinfection model that considered competition between isolates with an effect on transmission explained the invasion of the CMV population by N isolates at the beginning of the epidemic, and its predictions also agreed with field data on the long-term evolution of the CMV population. An important conclusion from both models was that the density of the aphid vector's population is a major factor in the evolution of CMV virulence. This may be relevant for the design of control strategies for CMV-induced diseases.

Biological Evolution↗
PubMed2005

Fate of mitochondrially located S19 ribosomal protein genes after transfer of a functional copy to the nucleus in cereals.

Mitochondrial genes for ribosomal proteins undergo relatively frequent transfer to the nucleus during plant evolution, and when migration is successful the mitochondrial copy becomes redundant and can be lost. We have examined the status of the mitochondrial rps19 gene for ribosomal protein S19 in closely related cereals. In oat, the mitochondrial rps19 reading frame is blocked by a premature termination codon and lacks abundant transcripts, whereas in the mitochondria of wheat and rye rps19 is a 5'-truncated pseudogene which is co-transcribed with the downstream nad4L gene. In barley and maize, rps19 sequences are completely absent from the mitochondrion. All five of these cereals differ from rice, in which an intact, transcriptionally active mitochondrial rps19 gene is found, and this is preceded by rpl2 in an organization reminiscent of that seen in bacteria. Based on EST sequence data for maize, barley and wheat, it can be inferred that a functional rps19 gene was transferred to the nucleus prior to the divergence of the maize and rice lineages (approximately 50 million years ago), and the present-day nuclear copies encode an N-terminal sequence related to the mitochondrial targeting signal of Hsp70 (heat shock protein) in cereals. Subsequent evolutionary events have included independent losses of the mitochondrial copies in the barley and maize lineages. In the rice lineage, on the other hand, the nuclear copy was lost. This is reflected in the persistence of the mitochondrial rps19 after a period during which rps19 genes coexisted in both compartments. These observations illustrate the dynamic nature of the location and structure of genes for mitochondrial ribosomal proteins in flowering plants.

Amino Acid Sequence↗
PubMed2001

Novel filaments 5 nm in diameter constitute the cytosolic ring of the plastid division apparatus.

The plastid division apparatus (called the plastid-dividing ring) has been detected in several plant and algal species at the constricted region of plastids by transmission electron microscopy. The apparatus is composed of two or three rings: an outer ring in the cytosol, an inner ring in the stroma, and a middle ring in the intermembrane space. The components of these rings are not clear. FtsZ, which forms the bacterial cytokinetic ring, has been proposed as a component of both the inner and outer rings. Here, we present the ultrastructure of the outer ring at high resolution. To visualize the outer ring by negative staining, we isolated dividing chloroplasts from a synchronized culture of a red alga, Cyanidioschyzon merolae, and lysed them with nonionic detergent Nonidet P-40. Nonidet P-40 extracted primarily stroma, thylakoids, and the inner and middle rings, leaving the envelope and outer ring largely intact. Negative staining revealed that the outer ring consists of a bundle of 5-nm filaments in which globular proteins are spaced 4.8 nm apart. Immunoblotting using an FtsZ-specific antibody failed to show immunoreactivity in the fraction containing the filament. Moreover, the filament structure and properties are unlike those of known cytoskeletal filaments. The bundle of filaments forms a very rigid structure and does not disassemble in 2 M urea. We also identified a dividing phase-specific 56-kD protein of chloroplasts as a candidate component of the ring. Our results suggest that the main architecture of the outer ring did not descend from cyanobacteria during the course of endosymbiosis but was added by the host cell early in plant evolution.

Actin Cytoskeleton↗
PubMedDate not supplied

Evolution of MADS-box gene induction by FLO/LFY genes.

Some MADS-box genes function as floral homeotic genes. The Arabidopsis LFY gene is a positive regulator of floral homeotic genes, and homologs of the FLO/LFY gene family in other angiosperms and gymnosperms are likely to have a similar function. To investigate the origin of the floral homeotic gene regulatory cascade involving the FLO/LFY gene, FLO/LFY homologs were cloned from a leptosporangiate fern (Ceratopteris richardii), two eusporangiate ferns (Angiopteris lygodiifolia and Botrychium multifidum var. robustum), three fern allies (Psilotum nudum, Equisetum arvense, and Isoetes asiatica), and a moss (Physcomitrella patens). The FLO/LFY gene phylogenetic tree indicates that both duplication and loss of FLO/LFY homologs occurred during the course of vascular plant evolution. The expression patterns of the Ceratopteris LFY genes (CrLFY1 and 2) were assessed. CrLFY1 expression was prominent in tissues including shoot tips and circinate reproductive leaves, but very weak in other tissues examined. Expression of CrLFY2 was also prominent in tissues, including shoot tips and circinate reproductive leaves. These patterns of expression are dissimilar to that of any Ceratopteris MADS-box gene previously reported, suggesting that the induction of MADS-box genes by FLO/LFY is not established at the stage of ferns.

Arabidopsis↗
PubMed2005

Gamma carbonic anhydrase like complex interact with plant mitochondrial complex I.

We report the identification by two hybrid screens of two novel similar proteins, called Arabidopsis thaliana gamma carbonic anhydrase like1 and 2 (AtgammaCAL1 and AtgammaCAL2), that interact specifically with putative Arabidopsis thaliana gamma Carbonic Anhydrase (AtgammaCA) proteins in plant mitochondria. The interaction region that was located in the N-terminal 150 amino acids of mature AtgammaCA and AtgammaCA like proteins represents a new interaction domain. In vitro experiments indicate that these proteins are imported into mitochondria and are associated with mitochondrial complex I as AtgammaCAs. All plant species analyzed contain both AtgammaCA and AtgammaCAL sequences indicating that these genes were conserved throughout plant evolution. Structural modeling of AtgammaCAL sequences show a deviation of functionally important active site residues with respect to gammaCAs but could form active interfaces in the interaction with AtgammaCAs. We postulate a CA complex tightly associated to plant mitochondrial complex.

Arabidopsis↗
PubMed1994

Chloroplast and cytosolic triosephosphate isomerases from spinach: purification, microsequencing and cDNA cloning of the chloroplast enzyme.

Chloroplast and cytosolic triosephosphate isomerases from spinach were separated and purified to homogeneity. Both enzymes were partially sequenced by Edman degradation. Using degenerate primers designed against the amino acid sequences, a homologous probe for the chloroplast enzyme was amplified and used to isolate several full-size cDNA clones. Chloroplast triosephosphate isomerase is encoded by a single gene in spinach. Analysis of the chloroplast cDNA sequence in the context of its homologues from eukaryotes and eubacteria reveals that the gene arose through duplication of its preexisting nuclear counterpart for the cytosolic enzyme during plant evolution.

Amino Acid Sequence↗
PubMed1997

An interspecific backcross of Lycopersicon esculentum x L. hirsutum: linkage analysis and a QTL study of sexual compatibility factors and floral traits.

A BC1 population of the self-compatible tomato Lycopersicon esculentum and its wild self-incompatible relative L. hirsutum f. typicum was used for restriction fragment length polymorphism linkage analysis and quantitative trait loci (QTL) mapping of reproductive behavior and floral traits. The self-incompatibility locus, S, on chromosome 1 harbored the only QTL for self-incompatibility indicating that the transition to self-compatibility in the lineage leading to the cultivated tomato was primarily the result of mutations at the S locus. Moreover, the major QTL controlling unilateral incongruity also mapped to the S locus, supporting the hypothesis that self-incompatibility and unilateral incongruity are not independent mechanisms. The mating behavior of near-isogenic lines carrying the L. hirsutum allele for the S locus on chromosome 1 in an otherwise L. esculentum background support these conclusions. The S locus region of chromosome 1 also harbors most major QTL for several floral traits important to pollination biology (e.g., number and size of flowers), suggesting a gene complex controlling both genetic and morphological mechanisms of reproduction control. Similar associations in other flowering plants suggest that such complex may have been conserved since early periods of plant evolution or else reflect a convergent evolutionary process.

Chromosome Mapping↗
PubMed1994

Plant delta-aminolevulinic acid dehydratase. Expression in soybean root nodules and evidence for a bacterial lineage of the Alad gene.

We isolated a soybean (Glycine max) cDNA encoding the heme and chlorophyll synthesis enzyme delta-aminolevulinic acid (ALA) dehydratase by functional complementation of an Escherichia coli hemB mutant, and we designated the gene Alad. ALA dehydratase was strongly expressed in nodules but not in uninfected roots, although Alad mRNA was only 2- to 3-fold greater in the symbiotic tissue. Light was not essential for expression of Alad in leaves of dark-grown etiolated plantlets as discerned by mRNA, protein, and enzyme activity levels; hence, its expression in subterranean nodules was not unique in that regard. The data show that soybean can metabolize the ALA it synthesizes in nodules, which argues in favor of tetrapyrrole formation by the plant host in that organ. Molecular phylogenetic analysis of ALA dehydratases from 11 organisms indicated that plant and bacterial enzymes have a common lineage not shared by animals and yeast. We suggest that plant ALA dehydratase is descended from the bacterial endosymbiont ancestor of chloroplasts and that the Alad gene was transferred to the nucleus during plant evolution.

Amino Acid Sequence↗
PubMed1991

Secondary structure as a constraint on the evolution of a plant viral satellite RNA.

The genetic variability and evolution of the satellite RNA (satRNA) of cucumber mosaic virus (CMV) was analyzed. Twenty-five CMV-satRNAs compared clustered into three main groups, and no correlation was found between genetic proximity and other characteristics (pathogenicity, geographical origin) of the satRNAs. Values for the number of nucleotide substitutions per site between any two satRNAs suggest that divergence is checked by functional constraints. The analysis of mutations relative to an ancestral sequence, and the number of substitutions per site at first, second and third positions of codons in putative open reading frames, show that the variation of CMV-satRNAs does not follow a pattern typical of coding sequences, and indicates that preservation of the sequence of encoded products is not a constraint to evolution. On the other hand, when the observed variation was analyzed relative to a secondary structure model proposed for CMV-satRNAs, several lines of evidence indicated that the maintenance of the secondary structure is a constraint to evolution: the number of substitutions per site, the number of point insertions and deletions and the number of base substitutions that would disrupt base-pairing were significantly higher for unpaired than for base-paired positions. Also, compensatory mutations at base-paired positions occurred more frequently than expected from random. The results suggest that CMV-satRNAs are non-coding, functional RNAs whose biology would be determined by their direct interaction with components of the host and/or the helper virus.

Base Composition↗
PubMed2000

Molecular characterisation of RecQ homologues in Arabidopsis thaliana.

Members of the RecQ family of DNA helicases are involved in processes linked to DNA replication, DNA recombination and gene silencing. RecQ homologues of various animals have been described recently. Here, for the first time for plants, we characterised cDNAs of all in all six different RecQ-like proteins that are expressed to different extents in Arabidopsis thaliana. Surprisingly, three of these proteins are small in size [AtRecQl1, AtRecQl2, AtRecQl3-606, 705 and 713 amino acids (aa), respectively], whereas the two bigger proteins result from a duplication event during plant evolution [AtRecQl4A and AtRecQl4B-1150 and 1182 aa, respectively]. Another homologue (AtRecQsim, 858 aa) most probably arose by insertion of an unrelated sequence within its helicase domain. The presence of these homologues demonstrates the conservation of RecQ family functions in higher eukaryotes. We also detected a small gene (AtWRNexo) encoding 285 aa which, being devoid of any RecQ-like helicase domain, reveals a striking homology to the exonuclease domain of human Werner protein, a prominent RecQ helicase of larger size. By means of the two-hybrid assay we were able to detect an interaction between AtWRNexo and AtRecQl2, indicating that activities that reside in a single protein chain in mammals might in plants be complemented in trans.

Adenosine Triphosphatases↗
PubMed2004

The class III peroxidase multigenic family in rice and its evolution in land plants.

Plant peroxidases (class III peroxidases, E.C. 1.11.1.7) are secreted glycoproteins known to be involved in the mechanism of cell elongation, in cell wall construction and differentiation, and in the defense against pathogens. They usually form large multigenic families in angiosperms. The recent completion of rice (Oryza sativa japonica c.v. Nipponbare) genome sequencing allowed drawing up the full inventory of the genes encoding class III peroxidases in this plant. We found 138 peroxidase genes distributed among the 12 rice chromosomes. In contrast to several other gene families studied so far, peroxidase genes are twice as numerous in rice as in Arabidopsis. This large number of genes results from various duplication events that were tentatively traced back using a phylogenetic tree based on the alignment of conserved amino acid sequences. We also searched for peroxidase encoding genes in the major phyla of plant kingdom. In addition to gymnosperms and angiosperms, sequences were found in liverworts, mosses and ferns, but not in unicellular green algae. Two rice and one Arabidopsis peroxidase genes appeared to be rather close to the only known sequence from the liverwort Marchantia polymorpha. The possible relationship of these peroxidases with the putative ancestor of peroxidase genes is discussed, as well as the connection between the development of the class III peroxidase multigenic family and the emergence of the first land plants.

Amino Acid Sequence↗
PubMed1992

The 1-aminocyclopropane-1-carboxylate synthase gene family of Arabidopsis thaliana.

Genomic sequences encoding five divergent 1-aminocyclopropane-1-carboxylic acid (ACC) synthase polypeptides (ACC1, ACC2, ACC3, ACC4, and ACC5) have been isolated from Arabidopsis thaliana by using heterologous cDNAs and PCR fragments amplified from genomic DNA with degenerate oligonucleotide primers. Each gene is located on a different chromosome in the Arabidopsis genome. The genes are differentially expressed during development and in response to environmental stimuli. Protein-synthesis inhibition derepresses the expression of all genes but most dramatically derepresses that of ACC2, suggesting that their expression may be under negative control. The sequence of ACC2 was determined, and its transcription initiation site was defined. Authenticity of the polypeptide encoded by the gene was confirmed by expression experiments in Escherichia coli. The predicted size of the protein is 55,623 Da, and it contains the 11 invariant amino acid residues conserved between aminotransferases and ACC synthases from various plant species. Comparative analysis of structural and expression characteristics of ACC synthase genes from Arabidopsis and other plant species suggests that the sequence divergence of the ACC synthase genes and possibly the distinct regulatory networks governing the expression of ACC synthase subfamilies arose early in plant evolution and before the divergence of monocots and dicots.

Amino Acid Sequence↗
PubMed1998

Plant NADP-dependent isocitrate dehydrogenases are predominantly localized in the cytosol.

The isoenzyme patterns of NADP-isocitrate dehydrogenase (NADP-IDH; EC 1.1.1.42) have been investigated in 15 species of higher plants using dietylaminoethyl ion-exchange chromatography and immunological techniques. The obtained results unambiguously demonstrate that the cytosolic enzyme is the predominant form in leaf extracts of all the surveyed plant species. The chloroplastic isoenzyme, previously reported in pea (Pisum sativum L.) leaves (R.D. Chen et al., 1989, Planta 178; 157-163), is a minor form in ferns and dicotyledonous angiosperms and is undetectable in gymnosperms and monocotyledonous angiosperms. Comparison of immunological relatedness suggests that the proteins of cytosolic isoenzymes have been highly conserved in the course of plant evolution. The data support the previously proposed idea that the cytosol is the major site for alpha-ketoglutarate production to be used for nitrogen assimilation.

Cytosol↗
PubMed2002

Lariat formation and a hydrolytic pathway in plant chloroplast group II intron splicing.

Lariat formation has been studied intensively only with a few self-splicing group II introns, and little is known about how the numerous diverse introns in plant organelles are excised. Several of these introns have branch-points that are not a single bulge but are adjoined by A:A, A:C, A:G and G:G pairs. Using a highly sensitive in vivo approach, we demonstrate that all but one of the barley chloroplast introns splice via the common pathway that produces a branched product. RNA editing does not improve domain 5 and 6 structures of these introns. The conserved branch-point in tobacco rpl16 is chosen even if an adjacent unpaired adenosine is available, suggesting that spatial arrangements in domain 6 determine correct branch-point selection. Lariats were not detected for the chloroplast trnV intron, which lacks an unpaired adenosine in domain 6. Instead, this intron is released as linear molecules that undergo further polyadenylation. trnV, which is conserved throughout plant evolution, constitutes the first example of naturally occurring hydrolytic group II intron splicing in vivo.

Chloroplasts↗