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Pattern formation in plant development: four vignettes.

In their development, plants precisely control the patterns of cell size, cell shape and cell division, the position of differentiation of cell types, and the position and number of organs. In the past year, progress has been made in understanding four of these five levels of control of plant pattern formation, including specification of cell fate by cell size in the alga Volvox carteri, genetic control of cell shape in the leaf hairs of the flowering plant Arabidopsis thaliana, precise control of cell division and cellular enlargement in Arabidopsis root meristems, and control of cell number in meristems of Arabidopsis, tobacco, and maize. These examples indicate that both the fate and shape of differentiated plant cells can be determined by the size of their undifferentiated precursors, and that the primary effect of mutations that alter cell fate and cellular shape can be on cell size. Furthermore, specific genes have been found that are necessary for normal patterns and numbers of cell divisions. Molecular cloning of these genes is revealing the molecular basis of plant cell division control.

Arabidopsis↗

Identification of higher plant GlsA, a putative morphogenesis factor of gametic cells.

GlsA has been identified in an asexual-reproductive-cell (gonidia)-deficient mutant of Volvox as a chaperone-like protein essential for gonidia production. In this study, we isolated an angiosperm glsA (LlglsA) gene expressed during Lilium longiflorum pollen development. Immunoblot analyses showed that the strong LlGlsA expression occurred in the generative cell and its pattern during pollen development corresponded to that of alpha-tubulin. Morphological analyses succeeded in visualizing the dispersion of the strong LlGlsA signal in developing generative cells. In addition, multiple-immunofluorescence staining of LlGlsA and alpha-tubulin revealed that some of the dot-like LlGlsA signals were co-localized with microtubule filaments. From those results, we suggest that angiosperm GlsA functions as a chaperone modifying various structures during male gametic cell formation.

Algal Proteins↗

The Chlorella hexose/H(+)-symporters.

The physiology, molecular biology, and biochemistry of the inducible hexose uptake protein of Chlorella kessleri is reviewed. The protein encoded by the HUP1 gene is the most intensively studied membrane transporter of plants. Responsible for substrate accumulation up to 1500-fold, it translocates one proton together with one hexose, and the cell invests 1 ATP per sugar transported. Kinetics suggest that substrate accumulation is mainly brought about by a large delta Km (Kminside >> Kmoutside). The HUP1 protein (534aa) consists of 12 transmembrane helices of which at least helices I, V, VII, and XI interact with the sugar during translocation and participate in lining the transport path through the membrane. The helix packing might very well be identical to the one suggested for the E. coli lac permease, although the mechanism for transport and proton coupling that has been suggested for lac permease (Kaback, 1997) certainly does not hold for the Chlorella symporter; both are distantly related members, however, of the MFS-family of transporters. HUP1 has been functionally expressed in Schizosaccharomyces pombe, Saccharomyces cerevisiae, Escherichia coli, Volvox carteri, and in Xenopus oocytes.

Amino Acid Sequence↗

Evolution of rbcL group IA introns and intron open reading frames within the colonial Volvocales (Chlorophyceae).

Mobile group I introns sometimes contain an open reading frame (ORF) possibly encoding a site-specific DNA endonuclease. However, previous phylogenetic studies have not clearly deduced the evolutionary roles of the group I intron ORFs. In this paper, we examined the phylogeny of group IA2 introns inserted in the position identical to that of the chloroplast-encoded rbcL coding region (rbcL-462 introns) and their ORFs from 13 strains of five genera (Volvox, Pleodorina, Volvulina, Astrephomene, and Gonium) of the colonial Volvocales (Chlorophyceae) and a related unicellular green alga, Vitreochlamys. The rbcL-462 introns contained an intact or degenerate ORF of various sizes except for the Gonium multicoccum rbcL-462 intron. Partial amino acid sequences of some rbcL-462 intron ORFs exhibited possible homology to the endo/excinuclease amino acid terminal domain. The distribution of the rbcL-462 introns is sporadic in the phylogenetic trees of the colonial Volvocales based on the five chloroplast exon sequences (6021 bp). Phylogenetic analyses of the conserved intron sequences resolved that the G. multicoccum rbcL-462 intron had a phylogenetic position separate from those of other colonial volvocalean rbcL-462 introns, indicating the recent horizontal transmission of the intron in the G. multicoccum lineage. However, the combined data set from conserved intron sequences and ORFs from most of the rbcL-462 introns resolved robust phylogenetic relationships of the introns that were consistent with those of the host organisms. Therefore, most of the extant rbcL-462 introns may have been vertically inherited from the common ancestor of their host organisms, whereas such introns may have been lost in other lineages during evolution of the colonial Volvocales. In addition, apparently higher synonymous substitutions than nonsynonymous substitutions in the rbcL-462 intron ORFs indicated that the ORFs might evolve under functional constraint, which could result in homing of the rbcL-462 intron in cases of spontaneous intron loss. On the other hand, the presence of intact to largely degenerate ORFs of the rbcL-462 introns within the three isolates of Gonium viridistellatum and the rare occurrence of the ORF-lacking rbcL-462 intron suggested that the ORFs might degenerate to result in the spontaneous intron loss during a very short evolutionary time following the loss of the ORF function. Thus, the sporadic distribution of the rbcL-462 introns within the colonial Volvocales can be largely explained by an equilibrium between maintenance of the introns by the intron ORF and spontaneous loss of introns when the introns do not have a functional ORF.

Amino Acid Sequence↗

Extrinsic proteins of photosystem II: an intermediate member of PsbQ protein family in red algal PS II.

The oxygen-evolving photosystem II (PS II) complex of red algae contains four extrinsic proteins of 12 kDa, 20 kDa, 33 kDa and cyt c-550, among which the 20 kDa protein is unique in that it is not found in other organisms. We cloned the gene for the 20-kDa protein from a red alga Cyanidium caldarium. The gene consists of a leader sequence which can be divided into two parts: one for transfer across the plastid envelope and the other for transfer into thylakoid lumen, indicating that the gene is encoded by the nuclear genome. The sequence of the mature 20-kDa protein has low but significant homology with the extrinsic 17-kDa (PsbQ) protein of PS II from green algae Volvox Carteri and Chlamydomonas reinhardtii, as well as the PsbQ protein of higher plants and PsbQ-like protein from cyanobacteria. Cross-reconstitution experiments with combinations of the extrinsic proteins and PS IIs from the red alga Cy. caldarium and green alga Ch. reinhardtii showed that the extrinsic 20-kDa protein was functional in place of the green algal 17-kDa protein on binding to the green algal PS II and restoration of oxygen evolution. From these results, we conclude that the 20-kDa protein is the ancestral form of the extrinsic 17-kDa protein in green algal and higher plant PS IIs. This provides an important clue to the evolution of the oxygen-evolving complex from prokaryotic cyanobacteria to eukaryotic higher plants. The gene coding for the extrinsic 20-kDa protein was named psbQ' (prime).

Amino Acid Sequence↗

Flows driven by flagella of multicellular organisms enhance long-range molecular transport.

Evolution from unicellular organisms to larger multicellular ones requires matching their needs to the rate of exchange of molecular nutrients with the environment. This logistic problem poses a severe constraint on development. For organisms whose body plan is a spherical shell, such as the volvocine green algae, the current (molecules per second) of needed nutrients grows quadratically with radius, whereas the rate at which diffusion alone exchanges molecules grows linearly, leading to a bottleneck radius beyond which the diffusive current cannot meet metabolic demands. By using Volvox carteri, we examine the role that advection of fluid by the coordinated beating of surface-mounted flagella plays in enhancing nutrient uptake and show that it generates a boundary layer of concentration of the diffusing solute. That concentration gradient produces an exchange rate that is quadratic in the radius, as required, thus circumventing the bottleneck and facilitating evolutionary transitions to multicellularity and germ-soma differentiation in the volvocalean green algae.

Animals↗

copia-like retrotransposons are ubiquitous among plants.

Transposable genetic elements are assumed to be a feature of all eukaryotic genomes. Their identification, however, has largely been haphazard, limited principally to organisms subjected to molecular or genetic scrutiny. We assessed the phylogenetic distribution of copia-like retrotransposons, a class of transposable element that proliferates by reverse transcription, using a polymerase chain reaction assay designed to detect copia-like element reverse transcriptase sequences. copia-like retrotransposons were identified in 64 plant species as well as the photosynthetic protist Volvox carteri. The plant species included representatives from 9 of 10 plant divisions, including bryophytes, lycopods, ferns, gymnosperms, and angiosperms. DNA sequence analysis of 29 cloned PCR products and of a maize retrotransposon cDNA confirmed the identity of these sequences as copia-like reverse transcriptase sequences, thereby demonstrating that this class of retrotransposons is a ubiquitous component of plant genomes.

Amino Acid Sequence↗

The Hematopoietic Microenvironment: Phylogeny and Ontogeny of the Hematopoietic Microenvironment.

Although there is no formalized area of study called phylogeny or ontogeny of the hematopoietic microenvironment, new models and molecular tools are now available for such studies. The concept of a hematopoietic microenvironment has developed from the need to answer basic questions about migration, control of proliferation and differentiation of lymphohematopoietic cells; e.g. how are cells with the same genes induced to express different sets of these genes which lead to differentiation. These questions were first approached when cells could only be identified morphologically. The ontogeny of hematopoiesis was traced from the blood islands of the embryonic yolk sac, to the fetal liver, spleen, and bone marrow. Cells with reticular morphology were associated with areas of hematopoiesis and, in the embryo, they were thought to give rise to both hematopoietic and supportive cells. In the 1960's the classic work of McCulloch, Till and Siminovitch led the study of hematopoietic precursors which have no distinctive morphological identity and are too infrequent to study microscopically. These cells were identified by their functions; e.g. colony formation in culture in the presence of certain factors, production of spleen colonies or rescue of lethally irradiated mice. Cells with these functions were also found sequentially in the yolk sac blood islands, in the aorta/mesonephros, fetal liver, spleen, and bone marrow during development. The question remained, what regulates the proliferation and differentiation of these cells and why do they home to different sites in different stages of development? Among the laboratories studying spleen colonies, a controversy arose as to whether differentiation decisions were stochastic or induced by extra cellular factors. Dexter and Greenberger developed the long-term bone marrow culture system which has aided in studying the roles of factors such as cell-cell contact and extracellular matrix in hematopoietic differentiation. The molecular identification of ligand/receptor pairs such as ckit and KL as well as transactivating factors that control whole sets of lineage related genes such as the GATAs and Ikaros, may lead to clarification of the stochastic versus induced differentiation issue. Chimeric bird and frog embryos and analysis of mutations effecting hematopoiesis in frogs and zebrafish have helped to trace the earliest hematopoietic development in the embryo and to determine what influences it. The identification of genes that alter development of hematopoiesis opens the possibility of comparing microenvironmental control mechanisms in various present day organisms and relating these to evolutionary events. Many basic questions relevant to the interaction between hematopoietic cells and their microenvironment can be addressed by studying "simple" organisms in which the answers may be more easily determined than in mice or humans. Examples of possibly useful organisms, range from the teliosts such as zebrafish to algae such as Volvox, a two cell organism, to Dictyostelium which change from 1 to many cell types and in the process, migrate, adhere and differentiate.

Journal Article↗

Structurally divergent histone H1 variants in chromosomes containing highly condensed interphase chromatin.

Condensed and late-replicating interphase chromatin in the Dipertan insect Chironomus contains a divergent type of histone H1 with an inserted KAP-KAP repeat that is conserved in single H1 variants of Caenorhabditis elegans and Volvox carteri. H1 peptides comprising the insertion interact specifically with DNA. The Chironomid Glyptotendipes exhibits a corresponding correlation between the presence of condensed chromosome sections and the appearance of a divergent H1 subtype. The centromere regions and other sections of Glyptotendipes barbipes chromosomes are inaccessible to immunodecoration by anti-H2B and anti-H1 antibodies one of which is known to recognize nine different epitopes in all domains of the H1 molecule. Microelectrophoresis of the histones from manually isolated unfixed centromeres revealed the presence of H1 and core histones. H1 genes of G. barpipes were sequenced and found to belong to two groups. H1 II and H1 III are rather similar but differ remarkably from H1 I. About 30% of the deduced amino acid residues were found to be unique to H1 I. Most conspicuous is the insertion, SPAKSPGR, in H1 I that is lacking in H1 II and H1 III and at its position gives rise to the sequence repeat SPAKSPAKSPGR. The homologous H1 I gene in Glyptotendipes salinus encodes the very similar repeat TPAKSPAKSPGR. Both sequences are structurally related to the KAPKAP repeat in H1 I-1 specific for condensed chromosome sites in Chironomus and to the SPKKSPKK repeat in sea urchin sperm H1, lie at almost the same distance from the central globular domain, and could interact with linker DNA in packaging condensed chromatin.

Amino Acid Sequence↗

The uni chromosome of Chlamydomonas: histone genes and nucleosome structure.

The uni linkage group (ULG) of Chlamydomonas reinhardtii contains many genes involved in the basal body-flagellar system. Recent evidence suggests that the corresponding uni chromosome is located in close proximity to the basal body complex. In the course of studies into its molecular organization, we have found a cluster of four histone genes on the ULG. The genes are arranged as divergently-transcribed pairs: H3-H4 and H2B-H2A. Genomic sequencing reveals that these genes lack introns and contain characteristic 3' palindromes similar to those of animals. The predicted amino acid sequences are highly conserved across species, with greatest similarities to the histone genes of Volvox. Southern analysis shows that each histone gene is present in 15-20 copies in Chlamydomonas and suggests a dispersed genomic organization. Northern analysis of mitotically-synchronized cells shows that, like the replication-dependent histones of higher eukaryotes, Chlamydomonas histone genes are expressed during S-phase. Using a gene-specific probe on Northern blots, we provide evidence that the ULG H4 gene is regulated in the same manner as other Chlamydomonas histone genes. Finally, micrococcal nuclease protection experiments show that the uni chromosome itself associates with histone proteins and displays a conventional nucleosomal banding pattern.

Amino Acid Sequence↗

Purification and characterization of trimming glucosidase I from pig liver.

Trimming glucosidase I has been purified about 400-fold from pig liver crude microsomes by fractional salt/detergent extraction, affinity chromatography and poly(ethylene glycol) precipitation. The purified enzyme has an apparent molecular mass of 85 kDa, and is an N-glycoprotein as shown by its binding to concanavalin A-Sepharose and its susceptibility to endo-beta-N-acetylglucosaminidase (endo H). The native form of glucosidase I is unusually resistant to non-specific proteolysis. The enzyme can, however, be cleaved at high, that is equimolar, concentrations of trypsin into a defined and enzymatically active mixture of protein fragments with molecular mass of 69 kDa, 45 kDa and 29 kDa, indicating that it is composed of distinct protein domains. The two larger tryptic fragments can be converted by endo H to 66 kDa and 42 kDa polypeptides, suggesting that glucosidase I contains one N-linked high-mannose sugar chain. Purified pig liver glucosidase I hydrolyzes specifically the terminal alpha 1-2-linked glucose residue from natural Glc3-Man9-GlcNAc2, but is inactive towards Glc2-Man9-GlcNAc2 or nitrophenyl-/methyl-umbelliferyl-alpha-glucosides. The enzyme displays a pH optimum close to 6.4, does not require metal ions for activity and is strongly inhibited by 1-deoxynojirimycin (Ki approximately 2.1 microM), N,N-dimethyl-1-deoxynojirimycin (Ki approximately 0.5 microM) and N-(5-carboxypentyl)-1-deoxynojirimycin (Ki approximately 0.45 microM), thus closely resembling calf liver and yeast glucosidase I. Polyclonal antibodies raised against denatured pig liver glucosidase I, were found to recognize specifically the 85 kDa enzyme protein in Western blots of crude pig liver microsomes. This antibody also detected proteins of similar size in crude microsomal preparations from calf and human liver, calf kidney and intestine, indicating that the enzymes from these cells have in common one or more antigenic determinants. The antibody failed to cross-react with the enzyme from chicken liver, yeast and Volvox carteri under similar experimental conditions, pointing to a lack of sufficient similarity to convey cross-reactivity.

Animals↗

The germline: familiar and newly uncovered properties.

Transplantations of both Drosophila pole cells and mouse primordial germ cells suggest that the pregonadal germline of these two organisms is not pluripotent. In mouse PGCs, however, the potential for activating pluripotency is clearly present, as seen in the relative case of deriving EG cells from migratory-stage PGCs. EG cells are derived from altering the in vitro growth conditions of PGCs by the addition of one factor. Conceivably, straying of PGCs in vivo could also lead to novel fates if they migrated into a suitable environment. Aberrant PGC migration underlies models for the origin of several tumor types. How are migratory-stage PGCs prevented from adopting alternative fates in wild-type development? One solution is to link accurate migration into the gonads with germ cell survival. One mechanism of accomplishing this is through the action of pleiotrophic factors such as Steel. Steel is both a proliferation and migration factor; sterility in Steel mutants is due to poor germ cell survival and improper migration. Networking of migratory PGCs is another mechanism to reduce the chances of individual germ cells straying from the migration path. Postmigratory germ cells apparently undergo another restriction on potency--novel imprinting. Assuming that EG methylation profiles accurately reflect modifications made in their founder PGCs, then "erased" pluripotent EG lines suggest that PGCs can be diverted from the germline lineage. Direct assays on PGCs show that the unmethylated phenotype at Igf2r region 2 is characteristic of late germ cells. The maintenance of germline-like methylation with a switch in PGC fate is somewhat analogous to the situation in lag mutants from Volvox, which retain large gonidial-sized cells that can nevertheless initiate somatic differentiation. Just as it is not possible to readjust cell size with a subsequent change in gonidial differentiation, it may be difficult, without gametogenesis, to reimpose methylation modifications once they have been erased. In addition, the methylation status of some sites/loci may be inconsequential to developmental gene activity in germ cells or EG cells. Recent studies indicate that the methylation imprint at Igf2r is not interpreted at functional level until embryogenesis (51). In summary, we have reviewed some distinctive properties of the development of germ cells, from their early segregation, mitotic and meiotic profile, sex determination, to their migration and sequestration into gonads. Some constraints on development of the germline likely serve to maintain its integrity until maturation, when the gametic genomes must be capable of initiating embryonic development. To accomplish this ultimate goal, germ cells in some organisms may retain a bias towards pluripotency throughout development.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

Reverse transcriptase-like sequences related to retrotransposon in a red alga, Porphyra yezoensis.

Four DNA fragments encoding a reverse transcriptase (RT)-like gene related to that of long terminal repeat (LTR) retrotransposons were isolated from the red alga Porphyra yezoensis by genomic PCR. Southern blot analysis suggested that one clone exists as a single copy per genome. Its full-length cDNA (PyRE2A) contained RT/RNase H-like sequences, which are most closely related to those of the Volvox LTR retrotransposon, although two stop codons were present within the RT region. We did not find any sequence related to LTR retrotransposons other than RT/RNase H in RyRE2A. These results indicate that PyRE2A is a single RT/RNase H-like gene and a defective progenitor of LTR retrotransposons.

Amino Acid Sequence↗

Maximum a posteriori estimation with Good's roughness for three-dimensional optical-sectioning microscopy.

The three-dimensional image-reconstruction problem solved here for optical-sectioning microscopy is to estimate the fluorescence intensity lambda(x), where x epsilon R3, given a series of Poisson counting process measurements [Mj(dx)]jJ = 1, each with intensity [formula: see text] with [formula: see text] being the point spread of the optics focused to the jth plane and sj(y) the detection probability for detector point y at focal depth j. A maximum a posteriori reconstruction generated by inducing a prior distribution on the space of images via Good's three-dimensional rotationally invariant roughness penalty [formula: see text] It is proven that the sequence of iterates that is generated by using the expectation maximization algorithm is monotonically increasing in posterior probability, with stable points of the iteration satisfying the necessary maximizer conditions of the maximum a posteriori solution. The algorithms were implemented on the DECmpp-SX, a 64 x 64 parallel processor, running at < 2 s/(64(3), 3-D iteration). Results are demonstrated from simulated as well as amoebae and volvox data. We study performance comparisons of the algorithms for the missing-data problems corresponding to fast data collection for rapid motion studies in which every other focal plane is removed and for imaging with limited detector areas and efficiency.

Algorithms↗

Total synthesis of chain-length-uniform dolichyl phosphates and their fitness to accept hexoses in the enzymatic formation of lipoglycans.

Dolichols of defined uniform chain length (C35, C45, and C55) and geometry were prepared by total synthesis according to the following principle: (E,E)-Farnesol, activated as its 4-tolyl sulfone, is condensed with 8-chloroneryl benzyl ether, the sulfonyl group removed and the ether linkage cleaved by lithium/triethylamine. The resulting elongated prenol is converted again to its corresponding 4-toly/sulfone; at this stage isomers are removed by chromatography. After several cycles of this C10-elongation sequence the synthesis is completed in the same way but using 8-chlorocitronellyl benzyl ether as building block to introduce the saturated alpha-isoprene unit. The dolichols obtained were chemically phosphorylated (POCl3/Et3N). Both, the alcohols and their phosphate esters, are characterized spectroscopically. 1H- and 13C-NMR data are recorded for qualitative and stereochemical comparison with natural dolichols. The authentic dolichyl phosphates (Dol-7-P, Dol-9-P, and Dol-11-P) were assayed relative to the natural dolichyl phosphate mixture from pig liver as acceptors for transglycosylation from nucleoside diphosphate sugars (glucose, mannose) by standardized membrane vesicle preparations from plants (Volvox) and animals (liver). Even the shortest chain dolichyl 7-phosphate has full activity in this lipoglycan-forming reaction.

Chemical Phenomena↗

Dolichyl phosphate-dependent glycosyltransferases utilize truncated cofactors.

Synthetic truncated dolichyl phosphates of chain lengths from four to thirteen isoprene units (Jaenicke L. and Siegmund H.-U., Chem. Phys. Lipids 51 (1989) 159-170) were assayed for their cofactor activity in the enzymatic transfer of hexoses and hexosamines. The enzymes were microsomal preparations from the green alga Volvox carteri, baker's yeast, and mammalian liver cells. Under saturating conditions, the acceptor activities of the truncated dolichyl phosphates increased from zero to full strength as compared to the mixture of long-chain dolichyl phosphates from natural sources with growing chain length from five to nine isoprene units. Km determinations confirmed the results. Of the geometric isomers of dolichyl 7-phosphate (35 carbon atoms), the 14-trans compound has unchanged acceptor activity; all-trans dolichyl 7-phosphate, however, was almost inactive. The data suggest that hydrophobicity may be an important, but not the only criterion for the binding of the isoprene moiety to the active sites of the transferase enzyme(s) and that the geometry of more than only one double bond in the dolichols is recognized.

Animals↗

The diet of Brycinus nurse (Pisces: Characidae) from Asa reservoir, Ilorin, Nigeria.

From November 1991 to October 1993, 980 specimens of the characid Brycinus nurse were collected from Asa reservoir to examine its diet. The diet was analyzed using the frequency of occurrence, numerical and gravimetric methods. Two hundred and sixty nine (27.45%) of the stomachs examined were empty. The fish was an omnivore feeding extensively on a wide array of plant and animal food items. These consisted of 9 families, 10 genera and 10 species. The most extensively consumed plant food item was aquatic plant parts which occurred in 63.88% of the stomachs, and accounted for 6.06% by number and 12.10% by weight while the ephemeropteran, Povilla adusta was the most dominant animal food item, occurring in 50.92% of the stomachs, and accounting for 11.98% by number and 11.86% by weight. Conversely, the least consumed plant food item was Volvox occurring in 4.49% of the stomachs and accounting for 0.18% by number and 0.35% by weight, while the fish Barbus sp. was the least consumed animal food item occurring in 0.51% of the stomachs, accounting for 0.03% by number and 1.62% by weight. New food items not previously recorded such as a watermite. Aspatharia sinuata and Barbus callipterus were found in the stomach contents. The nonspecific feeding regime of the fish and its ability to utilize different food items effectively was what accounted for the prominence and wide distribution of the fish in the lake.

Animals↗