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PubMed2003

The major clades of MADS-box genes and their role in the development and evolution of flowering plants.

MADS-box genes encode a family of transcription factors which control diverse developmental processes in flowering plants ranging from root to flower and fruit development. Sequencing of (almost) the complete Arabidopsis genome enabled the identification of (almost) all of the Arabidopsis MADS-box genes. MADS-box genes have been divided in two large groups, termed type I and type II genes. The type II genes comprise the MEF2-like genes of animals and fungi and the MIKC-type genes of plants. The majority of MIKC-type genes are of the MIKC(c)-type, which includes all plant MADS-box genes for which expression patterns or mutant phenotypes are known. By phylogeny reconstruction, almost all of the MIKC(c)-type genes can be subdivided into 12 major gene clades, each clade comprising 1-6 paralogs from Arabidopsis and putative orthologs from other seed plants. Here we first briefly describe the deep branching of the MADS-box gene tree to place the MIKC(c)-type genes into an evolutionary context. For every clade of MIKC(c)-type genes we then review what is known about its members from Arabidopsis and well-studied members from other phylogenetically informative plant species. By gene sampling and phylogeny reconstructions we provide minimal estimates for the ages of the different clades. It turns out that 7 of the 12 major gene clades, i.e., AG-, AGL6-, AGL12-, DEF+GLO- (B), GGM13- (B(s)), STMADS11- and TM3-like genes very likely existed already in the most recent common ancestor of angiosperms and gymnosperms about 300MYA. Three of the other clades, i.e., AGL2-, AGL17-, and SQUA-like genes, existed at least already in the most recent common ancestor of monocots and eudicots about 200 MYA. Only for two gene clades, AGL15-like genes (2 genes in Arabidopsis) and FLC-like genes (6 genes) members from plants other than Brassicaceae have not been reported yet. Similarly, only one ancient clade known from other flowering plant species, TM8-like genes, is not represented in Arabidopsis. These findings reveal that the diversity of MADS-box genes in Arabidopsis is rather ancient and representative for other flowering plants. Our studies may thus help to predict the set of MADS-box genes in all other flowering plants, except for relatively young paralogs. For the different gene clades we try to identify ancestral and derived gene functions and review the importance of these clades for seed plant development and evolution. We put special emphasis on gene clades for which insights into their importance has rapidly increased just recently.

Arabidopsis↗

PubMed2004

Metaxenia in the vine cacti Hylocereus polyrhizus and Selenicereus spp.

BACKGROUND AND AIMS: Flowers of the vine cacti of the genera Hylocereus and Selenicereus grown in Israel must be hand pollinated due to self-incompatibility and lack of efficient pollinators. In controlled pollination experiments, it was found that the time elapsed between pollination and ripening depends on the source of the pollen. Therefore a study was made of some effects of the pollen source on fruit development. METHODS: Flowers of Hylocereus polyrhizus were pollinated on the same day with different pollen sources and the stigmas were covered. Fruits were collected 4 d after reaching full colour. RESULTS: Pollinating flowers of Hylocereus polyrhizus with Selenicereus grandiflorus and S. megalanthus pollen delayed ripening by 1 and 3 weeks, respectively, as compared with ripening of fruits pollinated with Hylocereus undatus pollen. Other fruit characteristics affected by the pollen source were fruit size, pulp dry weight and number of seeds per fruit, all being significantly reduced, while peel dry weight was significantly increased by S. megalanthus pollen. Total soluble sugar content was reduced in H. polyrhizus fruits pollinated with S. grandiflorus pollen. No other major traits were affected. CONCLUSIONS: The results are evidence for the existence of metaxenia, i.e. an effect of pollen on maternal tissues, in cacti fruits. This pollen effect on the fruit-ripening time may be used for extending the marketing period of H. polyrhizus fruits.

Cactaceae↗

PubMed1999

Multiple sequence alignment: algorithms and applications.

Elucidation of interrelationships among sequence, structure, function, and evolution (FESS relationships) of a family of genes or gene products is a central theme of modern molecular biology. Multiple sequence alignment has been proven to be a powerful tool for many fields of studies such as phylogenetic reconstruction, illumination of functionally important regions, and prediction of higher order structures of proteins and RNAs. However, it is far too trivial to automatically construct a multiple alignment from a set of related sequences. A variety of methods for solving this computationally difficult problem are reviewed. Several important applications of multiple alignment for elucidation of the FESS relationships are also discussed. For a long period, progressive methods have been the only practical means to solve a multiple alignment problem of appreciable size. This situation is now changing with the development of new techniques including several classes of iterative methods. Today's progress in multiple sequence alignment methods has been made by the multidisciplinary endeavors of mathematicians, computer scientists, and biologists in various fields including biophysicists in particular. The ideas are also originated from various backgrounds, pure algorithmics, statistics, thermodynamics, and others. The outcomes are now enjoyed by researchers in many fields of biological sciences. In the near future, generalized multiple alignment may play a central role in studies of FESS relationships. The organized mixture of knowledge from multiple fields will ferment to develop fruitful results which would be hard to obtain within each area. I hope this review provides a useful information resource for future development of theory and practice in this rapidly expanding area of bioinformatics.

Algorithms↗

PubMed2002

Characterization of the peach homologue of the ethylene receptor, PpETR1, reveals some unusual features regarding transcript processing.

To identify which processes in peach, Prunus persica [L.] Batsch., are associated with changes in ethylene perception, we cloned and characterized a peach homologue of the gene encoding the ethylene receptor, ETR1. A fragment of the peach gene, PpETR1, obtained via PCR using degenerate primers against peach genomic DNA was used to screen a cDNA library made from ripening fruit. The resulting cDNA and subsequent 3' RACE clones indicate that the PpETR1 coding region is highly similar to other ETR1 homologues. However, the mRNA undergoes unusual alternative splicing that potentially results in three different mature transcripts. Use of an alternative 3' splice site to remove the last intron in PpETR1a results in a polypeptide that is missing three amino acids within the receiver-like domain. Retention of the terminal intron occurs in PpETR1b, which, if translated, would result in a truncated protein lacking a receiver-like domain. Fruit from three cultivars with substantially different ripening times were examined from 7 to 130 days after bloom using RT-PCR to characterize expression of the intron-retaining and fully spliced mRNAs. There were only slight differences in the abundance of these mRNAs among cultivars during fruit development; however, one of the slow-ripening cultivars showed a substantial increase in expression of the unspliced mRNA in pre-climacteric fruit. Variations in PpETR1 transcript abundance in wounding experiments indicate that the properly spliced and unspliced versions have different accumulation patterns in fruit, whereas both are essentially constitutive in leaves. These observations indicate that changes in ethylene sensitivity may occur during wounding in fruit.

Amino Acid Sequence↗

PubMed2001

Fruit-developmental regulation of bell pepper knolle gene (cakn) expression(1).

A cDNA, cakn, orthologous to the Arabidopsis KN gene, which is involved in vesicle fusion during cell plate formation, was isolated from bell pepper fruit. cakn seems to be monogenic and its expression mainly transcriptionally regulated. During fruit development, transcript and protein levels increase significantly in the early stages in which numerous cell divisions occur, but in the stages corresponding to fruit growth by cell enlargement, whereas the messengers are undetectable, proteins are still faintly present, suggesting a different stability rate for the two types of macromolecules.

Amino Acid Sequence↗

PubMed2001

Three MADS-box genes similar to APETALA1 and FRUITFULL from silver birch (Betula pendula).

Despite intensive research on genetic regulation of flower development there are still only a few studies on the early phases of this process in perennial plants like trees. The aim of this study has been to identify genes that regulate early stages of inflorescence development in silver birch (Betula pendula Roth) and to follow the expression of these genes during development of the unisexual birch inflorescences. Here we describe the cloning and characterization of 3 cDNAs representing MADS-box genes designated BpMADS3, BpMADS4 and BpMADS5, all belonging to the AP1/SQUA group of plant MADS-box genes. According to RNA blot analysis, all 3 genes are active during the development of both male and female inflorescences. However, differences in patterns of expression suggest that they play different roles. BpMADS3 is most similar in sequence to AP1 and SQUA, but it seems to have the highest expression at late developmental stages. BpMADS4 is most similar in sequence to the Arabidopsis gene FRUITFULL, but is expressed, in addition to developing inflorescences, in shoots and roots. BpMADS5 is also similar to FRUITFULL; its expression seems to be inflorescence-specific and continues during fruit development. Ectopic expression of either BpMADS3, BpMADS4 or BpMADS5 with the CaMV 35S promoter in tobacco results in extremely early flowering. All of these birch genes seem to act early during the transition to reproductive phase and might be involved in the determination of the identity of the inflorescence or flower meristem. They could apparently be used to accelerate flowering in various plant species.

Journal Article↗

PubMed1985

Diurnal water balance of the cowpea fruit.

The vascular network of the cowpea (Vigna unguiculata [L.] Walp.) fruit exhibits the anatomical potential for reversible xylem flow between seeds, pod, and parent plant. Feeding of cut shoots with the apoplast marker acid fuchsin showed that fruits imported regularly via xylem at night, less frequently in early morning, and only rarely in the afternoon. The dye never entered seeds or inner dorsal pod strands connecting directly to seeds. Root feeding (early morning) of intact plants with (32)PO(4) or (3)H(2)O rapidly (20 min) labeled pod walls but not seeds, consistent with uptake through xylem. Weak subsequent (4 hours) labeling of seeds suggested slow secondary exchange of label with the phloem stream to the fruit. Vein flap feeding of subtending leaves with [(14)C]sucrose, (3)H(2)O, and (32)PO(4) labeled pod and seed intensely, indicating mass flow in phloem to the fruit. Over 90% of the (14)C and (3)H of fruit cryopuncture phloem sap was as sucrose and water, respectively. Specific (3)H activities of transpired water collected from fruits and peduncles were assayed over 4 days after feeding (3)H(2)O to roots, via leaf flaps, or directly to fruits. The data indicated that fruits transpired relatively less xylem-derived (apoplastic) water than did peduncles, that fruit and peduncle relied more heavily on phloem-derived (symplastic) water for transpiration in the day than at night, and that water diffusing back from the fruit was utilized in peduncle transpiration, especially during the day. The data collectively support the hypothesis of a diurnally reversing xylem flow between developing fruit and plant.

Journal Article↗

PubMed1990

The Tomato Fruit Cell Wall : II. Polyuronide Metabolism in a Nonsoftening Tomato Mutant.

A nonsoftening tomato (Lycopersicon esculentum L.) variety, dg, was examined to assess the physiological basis for its inability to soften during ripening. Total uronic acid levels, 18 milligrams uronic acid/100 milligrams wall, and the extent of pectin esterification, 60 mole%, remained constant throughout fruit development in this mutant. The proportion of uronic acid susceptible to polygalacturonase in vitro also remained constant. Pretreatment of heat-inactivated dg fruit cell walls with tomato pectinmethylesterase enhances polygalacturonase susceptibility at all ripening stages. Pectinesterase activity of cell wall protein extracts from red ripe dg fruit was half that in extracts from analogous tissue of VF145B. Polygalacturonase activities of cell wall extracts, however, were similar in both varieties. Diffusion of uronic acid from tissue discs of both varieties increased beginning at the turning stage to a maximum of 2.0 milligrams uronic acid released/gram fresh weight at the ripe stage. The increased quantity of hydrolytic products released during ripening suggests the presence of in situ polygalacturonase activity. Low speed centrifugation was employed to induce efflux of uronide components from the cell wall tree space. In normal fruit, at the turning stage, 2.1 micrograms uronic acid/gram fresh weight was present in the eluant after 1 hour, and this value increased to a maximum of 8.2 micrograms uronic acid/gram fresh weight at the red ripe stage. However, centrifuge-aided extraction of hydrolytic products failed to provide evidence for in situ polygalacturonase activity in dg fruit. We conclude that pectinesterase and polygalacturonase enzymes are not active in situ during the ripening of dg fruit. This could account for the maintenance of firmness in ripe fruit tissue.

Journal Article↗

PubMed2000

Molecular cloning and characterization of a novel gene encoding limonoid UDP-glucosyltransferase in Citrus.

We isolated a cDNA clone encoding limonoid UDP-glucosyltransferase (limonoid GTase) from the albedo of Satsuma mandarin (Citrus unshiu Marc.) and investigated the contribution to limonoid glucoside accumulation in fruit. The isolated cDNA clone (CitLGT) was 1732 bp in length encoding 511 deduced amino acids with a predicted molecular mass of 57.5 kDa. The products of in vitro translation from an expression vector had the limonoid GTase activity. Southern blot analysis of genomic DNA indicated that CitLGT was present as a single copy gene in the Citrus genome. The amount of transcript corresponding to CitLGT mRNA changed the same way as the fluctuation of limonin glucoside content during fruit development of navel orange (Citrus sinensis Osb.). This indicates that the transcription of CitLGT regulates the conversion of limonoid aglycones to glucosides in citrus fruit.

Amino Acid Sequence↗

PubMed2000

The gene pat-2, which induces natural parthenocarpy, alters the gibberellin content in unpollinated tomato ovaries.

We investigated the role of gibberellins (GAs) in the effect of pat-2, a recessive mutation that induces facultative parthenocarpic fruit development in tomato (Lycopersicon esculentum Mill.) using near-isogenic lines with two different genetic backgrounds. Unpollinated wild-type Madrigal (MA/wt) and Cuarenteno (CU/wt) ovaries degenerated, but GA(3) application induced parthenocarpic fruit growth. On the contrary, parthenocarpic growth of MA/pat-2 and CU/pat-2 fruits, which occurs in the absence of pollination and hormone application, was not affected by GA(3). Pollinated MA/wt and parthenocarpic MA/pat-2 ovary development was negated by paclobutrazol, and this inhibitory effect was counteracted by GA(3). The main GAs of the early-13-hydroxylation pathway (GA(1), GA(3), GA(8), GA(19), GA(20), GA(29), GA(44), GA(53), and, tentatively, GA(81)) and two GAs of the non-13-hydroxylation pathway (GA(9) and GA(34)) were identified in MA/wt ovaries by gas chromatography-selected ion monitoring. GAs were quantified in unpollinated ovaries at flower bud, pre-anthesis, and anthesis. In unpollinated MA/pat-2 and CU/pat-2 ovaries, the GA(20) content was much higher (up to 160 times higher) and the GA(19) content was lower than in the corresponding non-parthenocarpic ovaries. The application of an inhibitor of 2-oxoglutarate-dependent dioxygenases suggested that GA(20) is not active per se. The pat-2 mutation may increase GA 20-oxidase activity in unpollinated ovaries, leading to a higher synthesis of GA(20), the precursor of an active GA.

Genes, Plant↗

PubMed2002

Hironoia fusiformis gen. et sp. nov.; a cornalean fruit from the Kamikitaba locality (Upper Cretaceous, Lower Coniacian) in northeastern Japan.

The application of sieving techniques to bulk samples from the Ashizawa Formation, Futaba Group (Lower Coniacian) of northeastern Honshu, Japan, has yielded well-preserved mesofossil assemblages comparable with those recently described from eastern North America, Europe, and central Asia. Among the most abundant and distinctive components of these assemblages are fusiform fruits that are assigned here to a new genus and species, Hironoia fusiformis gen. et sp. nov. The fruits developed from an epigynous ovary with three to four locules. Each locule bears one seed and has a distinctive dorsal germination valve. These features of the fruit, along with the adnate calyx, indicate an affinity to extant Cornales and specifically the Cornaceae sensu lato. The recognition of an unequivocal cornalean fruit in the Early Coniacian-Early Santonian of Japan provides the earliest record of this group in the fossil record. It also establishes a minimum age for the early divergence of the asterid clade, a major group of living angiosperms comprising more than a third of all species of extant flowering plants.

Journal Article↗

PubMed1997

Characterization of ppEG1, a member of a multigene family which encodes endo-beta-1,4-glucanase in peach.

Three cDNA clones (pCel 10, pCel 20 and pCel 30), each encoding different endo-beta-1,4-glucanases in peach, were obtained by RT-PCR and their expression investigated by northern analysis during leaf and fruit abscission and during fruit development. This analysis allowed the detection of only the pCel 10-related mRNA. A 2.2 kb transcript accumulated in ethylene activated abscission zones of leaves and fruits, and ppEG1 (Prunus persica endoglucanase 1) the gene coding for pCel 10, was isolated and characterized. A cDNA (termed pCel 1), containing the entire open reading frame of ppEGC1, was obtained and its sequence used to define the structure of the gene and the exon/intron boundaries. ppEG1 consists of 7 exons and encodes a 497 amino acid polypeptide including a putative signal peptide at the N-terminus. The similarity of this peach endo-beta-1,4-glucanase (EGase, EC 3.2.1.4) is high (76.3%) with the ripening avocado and low (47.3%) with the bean abscission EGase. A 1639 bp region at the 5' of the transcription start site shows regulatory functions in transgenic tobacco plants, as judged by its ability to drive GUS expression in cell separation-related events.

Amino Acid Sequence↗

PubMed2000

MDH1: an apple homeobox gene belonging to the BEL1 family.

Differential display was used to isolate genes differentially expressed early in fruit development of apple (Malus domestica Borkh.). This approach resulted in the isolation of MDH1, a homeobox gene with a homeodomain similar to that of BELL1 (BEL1), which is involved in regulation of ovule development in Arabidopsis. However, outside the homeodomain MDH1 is quite different from BEL1. In apple, MDH1 mRNA was predominantly found in flowers, expanding leaves and expanding fruit. In pre-anthesis flowers, in situ hybridization showed that MDH1 mRNA accumulated in ovules. To further investigate the function of this new homeobox gene, MDH1 was transformed into Arabidopsis thaliana under the control of the cauliflower mosaic virus 35S promoter. The transgenic Arabidopsis plants showed dwarfing, reduced fertility and changes in carpel and fruit (silique) shape. The size and shape of the cells in the transgenic fruit was irregular. Both the transgenic phenotypes in Arabidopsis and the expression pattern of this gene in apple are consistent with the idea that MDH1 is likely to play an important role in control of plant fertility.

Amino Acid Sequence↗

PubMed2001

Bimodal patterns of floral gene expression over the two seasons that kiwifruit flowers develop.

Polymerase chain reaction fragments with homology to the Arabidopsis floral meristem identity genes LEAFY and APETALA1 have been isolated from kiwifruit (Actinidia deliciosa [A. Chev.] C. F. Liang and A. R. Ferguson) and have been named ALF and AAP1, respectively. Northern hybridisation analyses have shown that ALF and AAP1 have bimodal patterns of annual expression in developing first-order axillary buds and their subsequent shoots. This pattern of expression is consistent with the 2-year cycle of axillary bud, flower and fruit development observed in kiwifruit. The first period of expression was early in first-order bud development (late spring of the first growing season), when second-order meristems are initiated, and the second, approximately 10 months later, when those meristems differentiate flowers (late spring of the second growing season). In situ hybridisation analyses on axillary buds collected during late spring of the first growing season have shown ALF expression throughout the developing first-order buds and AAP1 expression was localised in developing second-order axillary meristems. During the spring of the second growing season, transcript accumulation for both ALF and AAP1 is localised in differentiating flowers. Our results show that important developmental events are occurring very early in kiwifruit first-order axillary bud development (spring of the first growing season) and it is likely that this includes floral commitment (evocation).

Journal Article↗

PubMed1983

The organisation of fruiting body formation in Dictyostelium minutum.

The process of culmination was investigated in three strains of the species Dictyostelium minutum. After aggregates have been formed a pulsatile signalling mechanism arises; the centre of signal emission becomes the apex of the developing fruiting structure. In the late aggregate, all cells differentiate into prespore cells. Cells that have reached the apex of the culminating cells mass redifferentiate into stalk cells. In two of the three D. minutum strains, interruption of regular stalk formation, more or less random formation of stalk cells and the synthesis of stalk supporting material from cell debris often takes place. The formation of multiple apices on aggregates and early fruiting structures is characteristic for these two strains. Within the species D. minutum, the exhibition of a marked pulsatile signalling mechanism is correlated with a capacity to form a regularly shaped stalk and to organize relatively large cell masses. The possible function of pulsatile signalling in the culmination process is discussed.

Cell Differentiation↗

PubMed1989

Heat shock protein hsp70 cognate gene expression in vegetative and reproductive organs of Lycopersicon esculentum.

We have detected hsc70 gene expression (heat shock protein hsp70 cognate) during vegetative growth and reproductive development in tomato (Lycopersicon esculentum). Using RNA from a tomato hsc70 cDNA as a probe in in situ hybridizations, we have determined expression patterns of hsc70 in nonstressed tomato roots, stems, leaves, flowers, and developing fruits. We have localized high levels of hsc70 transcript to the vascular system of the ovary, dividing cells of the lateral root tips, and the inner integument of developing seeds. We also see expression in the transmitting tissue, in immature anthers, and in embryos. We cannot detect expression in mature pollen, xylem, or ovules. These data indicate that the expression of at least some tomato hsp70 family members is developmentally regulated.

Journal Article↗

PubMed2004

Developmental analysis of carbohydrate metabolism in tomato (Lycopersicon esculentum cv. Micro-Tom) fruits.

Carbohydrate metabolism during the development of fruits of the tomato cultivar Micro-Tom was studied. The metabolism of the pericarp and placental tissues was found to be different. Starch was degraded more slowly in the placenta in comparison with the pericarp, whereas soluble sugars accumulated to a greater extent in the pericarp. The activities of glycolytic enzymes tended to peak at 40 days after flowering. Two of these, phosphoenolpyruvate phosphatase and pyruvate kinase, showed a dramatic increase in activity just before this peak, possibly indicating a role in up-regulating glycolysis to generate increased ATP that would be used during climacteric respiration. The expression of plastidial transporters was studied. Both the TPT and Glu6P transporter were expressed greatest in green fruits, before declining. The expression of the triose-phosphate transporter was greater than that of the glucose 6-phosphate transporter. The ATP/ADP transporter was expressed to a low level throughout fruit development.

Journal Article↗

PubMed1997

Molecular cloning and characterization of a MADS-box cDNA clone of the Fuji apple.

A cDNA clone, MdMADS1, containing MADS domain was isolated from the Fuji apple. The gene was expressed in all floral organs and young fruits but not in leaves. The expression was higher at the early stages of flower and fruit developments, suggesting that MdMADS1 plays a major role in the initiation of reproductive organ developments.

Amino Acid Sequence↗