A Survey of Databases for Analysis of Plant Cell Wall-Related Enzymes

Biofuels derived from plant cell wall lignocellulose have the potential to serve as an alternative source of energy, relieving dependence on finite petroleum reserves and reducing production of climate-changing greenhouse gases. To better elucidate cell wall structure, the plant research community has developed databases to host the accumulated information on plant cell wall-related enzymes. The goal of this review is to provide a comprehensive catalog of these databases, as well as to describe the data and tools that they make available. A Directory of Databases for Plant Cell Wall-Related Enzymes (plantcellwalls.ucdavis.edu) was also developed to provide links to all the databases reviewed in this paper and relevant publications.     

Nucleolytic Enzymes in Growing Root Cells

Experimental material consisted of fifteen serial sections 1.0mm. in length, cut from the apex towards the base of bean rootsof standard length. Optimum pH for ribo- and deoxyribonucleaseswere determined. Each enzyme was assayed at optimum pH in correspondinggroups of sections, and the enzyme activity per cell calculated.Results are compared with those obtained using other tissuesand with those of earlier investigations of the enzyme complementof the bean root.     

Proteolytic Enzymes in Growing Root Cells

The experimental material consisted of fifteen serial sections,each 1·o mm. in length, cut from the apex towards thebase of the bean root. Proteolytic enzymes were assayed at variouspH levels on corresponding groups of sections. Values per sectionwere converted to average values per cell by dividing each bythe number of cells occurring in the section. Evidence was obtainedfor the presence of two proteolytic enzymes or groups of enzymeswith different pH optima. Maximum activity of proteolytic enzymesis shown by cells which have ceased to grow and in which thelevel of protein and certain other enzymes is falling. The significanceof these observations in the interpretation of a mechanism ofcell growth is discussed.     

Regulation of mRNAs for Three Enzymes in the Glial Cell Model C6 Cell Line

In the glial cell line C6, regulation of actinomycin D (Act-D)-sensitive translatable polysomal mRNAs of three key enzymes--glycerol phosphate dehydrogenase (GPDH; EC 1.1.1.8) and glutamine synthetase (GS) by glucocorticoids and lactate dehydrogenase (LDH; EC 1.1.1.27) by catecholamines--is described. Though the first two enzymes are hydrocortisone (HC)-inducible, the nature of their response to the hyperacetylating agent sodium butyrate is dramatically different. Furthermore the appearance of GPDH translatable poly(A)+ RNA in HC-induced cells is inhibited by the presence of cycloheximide (CHX), whereas the induction of GS is unaffected by CHX. These observations necessitate further probing into an existing model system to explain the varied mechanisms of induction of these two enzymes by a single inducer. In combination with the third enzyme whose induction by catecholamines is glial specific, we believe that the C6 cell represents the most appropriate cell line for molecular neurobiologists to study the mechanisms of hormone action in glia.     

Developmental Changes in Levels of Translatable mRNAs for Enolase Isozymes in Chicken Brain

Using chicken brain mRNAs, alpha and gamma enolase precursors were synthesized in the rabbit reticulocyte cell-free translation system. The product proteins showed molecular weights almost identical to those of the mature subunits. The levels of translatable mRNAs for alpha and gamma subunits were determined by the cell-free translation system and immunoprecipitation with specific antisera, during development of chicken brain. The level of alpha mRNA was high at any developmental stage of the brain. On the other hand, the gamma mRNA level was very low at the early embryonic stage, and increased rapidly during development of the brain. These changes were closely correlated with those of the corresponding enzyme activities, indicating that the levels of enolase activities in developing brain were controlled primarily by the level of the translatable alpha and gamma mRNAs.     

Cell Wall Synthesis by Chlamydia psittaci Growing in L Cells

Biochemical events accompanying changes in structure and behavior of the cell walls of Chlamydia psittaci strain 6BC during its developmental cycle in L cells (mouse fibroblasts) were studied by measuring at short intervals the effect of d-cycloserine and penicillin G on incorporation of labeled intermediates into acid-insoluble fractions of infected L cells in which host incorporation had been inhibited by cycloheximide and into intact chlamydial cells and cell walls separated from the infected L cells. d-Cycloserine enhanced the incorporation of (14)C-l-alanine at all times in the developmental cycle, but the incorporation of (14)C-l-lysine was always inhibited. In parallel experiments, penicillin G had no effect on incorporation of any of these intermediates, but when infected L cells incorporated (14)C-l-alanine in the presence of penicillin G, the labeled alanine was released more rapidly in the subsequent absence of the antibiotic than in its continued presence. When either penicillin G or d-cycloserine was present throughout the developmental cycle, C. psittaci continued to synthesize deoxyribonucleic acid and protein, but at less than normal rates.     

Levels of Cytokinins in the Ovules of Cotton Mutants with Altered Fiber Development

Endogenous levels of cytokinin and abscisic acid (ABA) were determined in ovules of normal cotton (TM-1) and four fiber differentiation mutants (n2, Ligon lintless, H10, and Xu142) before and after flowering by enzyme-linked immunosorbent assays. The fluctuation patterns of ABA levels in ovules of normal cotton and mutants were similar. At the fiber elongation stage, ABA content was low, and from 1 day after flowering, the ABA content decreased steadily. On the other hand, the peaks of isopentenyladenine and isopentenyladenosine in ovules of TM-1 were observed 1 day before flowering. The level of cytokinins decreased after flowering in TM-1, whereas in the mutants it increased steadily. These results indicate that endogenous ABA is probably not the main inhibitor for fiber elongation and that endogenous cytokinins likely play a dual role in fiber development. Before flowering, cytokinins function as one of the stimuli for the initiation of fibers, but after flowering, cytokinins inhibit fiber growth. Received February 18, 1997; accepted June 11, 1997     

Antioxidant Systems in Tumour Cells: The Levels of Antioxidant Enzymes, Ferritin, and Total Iron in a Human Hepatoma Cell Line

The human hepatoma cell line Hep 3B, which has the hepatitis B virus genome, shows over 80% decrease of copper/zinc superoxide dismutase activity, over 90% decrease of manganese superoxide dismutase activity, over 70% decrease of catalase activity, absence of glutathione peroxidase and glutathione S-transferase activities, over 270-fold increase of ferritin content and 25-fold increase of total iron compared to normal autopsy liver. These conditions of low antioxidant enzyme activities and iron overload are those which support the accumulation of oxygen free-radicals and DNA damage commonly considered to be carcinogenic mechanisms.     

Antioxidant Systems in Tumour Cells: The Levels of Antioxidant Enzymes,Ferritin, and Total Iron in a Human Hepatoma Cell Line

The human hepatoma cell line Hep 3B, which has the hepatitis B virus genome, shows over 80% decrease of copper/zinc superoxide dismutase activity, over 90% decrease of manganese superoxide dismutase activity, over 70% decrease of catalase activity, absence of glutathione peroxidase and glutathione S-transferase activities, over 270-fold increase of ferritin content and 25-fold increase of total iron compared to normal autopsy liver. These conditions of low antioxidant enzyme activities and iron overload are those which support the accumulation of oxygen free-radicals and DNA damage commonly considered to be carcinogenic mechanisms.     

果实软化的胞壁物质和水解酶变化

果实软化通常被认为是由于胞壁水解酶如多聚半乳糖醛酸酶,果胶酯酶,纤维素酶降解胞壁物质导致。本文概述了这三种酶分子与果实软化关系的研究进展。反义基因证明,这三种酶基因的任一种表达被报制,果实能够正常软化,暗示果实的软化有其它因子的参与。其中由细胞内的淀粉酶和蔗糖酶引起的细胞膨压的变化及果胶的溶解可能是引起果肉软化的重要原因。     

Changes in Activities of Glucose Metabolising Enzymes in Germ Cells during Spermatogenesis in Rats

The rate of ¹⁴CO₂, liberation from [¹⁴C-1]glucose was identical to that from [¹⁴C-6]glucose in spermatids, but more than the latter in spermatogonia. Rotenone (1 μM) completely inhibited ¹⁴CO₂ release from [¹⁴C-1]glucose in spermatids, but decreased it only 30% in spermatogonia. The activity of glucose-6-phosphate dehydrogenase, but not 6-phosphogluconate dehydrogenase, was markedly lower in spermatocytes and spermatids than in spermatogonia. The activities of the glycolytic enzymes, glucosephosphate isomerase, fructose diphosphatase, glyceraldehyde-3-phosphate dehydrogenase and enolase, differed only slightly in spermatids and spermatogonia. It is concluded that the low glucose-6-phosphate dehydrogenase activity may contribute to the low activity of the pentose cycle in spermatocytes and spermatids.     

Gibberellin-Induced Alterations to the Expression of Cell Wall-Related Genes in the Xylem of Carrot Root

Journal of Plant Growth Regulation - Gibberellins (GAs) are a group of plant hormones that play important roles in various processes. Previous studies demonstrated that GA can increase the...     

Extraction of Enzymes from Cell Walls of Sugar Beet Cells Grown in Suspension Culture

Various glycosidases were extracted from cell walls of sugarbeet cells grown in suspension culture using three successiveprocedures employing saline, EDTA, and commercial cellulase.Saline was effective for extracting acid invertase, ß-galactosidase,and ß-glucosidase. EDTA extracted most of the -galactosidaseand some of the ß-glucosidase. It was most effectivebetween 27?C and 40?C. Commercial cellulase could extract mostof the -mannosidase in the cell wall when used at 27?C for 96h. These three procedures could not extract some of the acidinvertase and ß-glucosidase. The results suggest thatthe cell wall glycosidases are associated with different polysaccharides. These extraction procedures were also applied to the cell wallsof intact tissues, such as cotyledons, hypocotyls plus roots,and mature roots of sugar beets. EDTA as well as saline wasquite effective for extracting bound enzymes from the cell wallof intact tissue, which indicated that extraction with EDTAis useful for liberating bound enzymes from plant cell walls. (Received October 19, 1987; Accepted March 16, 1988)     

Anatomical Changes in Prosopis tamarugo Phil. Seedlings Growing at Different Levels of NaCl Salinity

Seedlings of Prosopis tamarugo were grown in artificial substrateswith additions, of 200, 400 and 600 mM NaCl, and without salttreatment. Salinity induced anatomical changes in the roots,stems and leaflets. The diameters of the roots of seedlingsgrown in the increasing salt concentrations (up to 400 mM) wereprogressively smaller and differentiation of the stelar tissueswas delayed. At an NaCl concentration of 600 mM, the root structurewas strongly altered. On the contrary, stem diameter increasedas salinity rose. In the stems of seedlings grown in a concentrationof 200 mM NaCl, secondary xylem differentiation appeared earlierthan in the controls. At a concentration of 400 mM NaCl, disorganizationof the vascular cylinder of the stem was evident. Leaflets ofseedlings grown in 200 mM NaCl showed a delay in structuraldifferentiation: no water-storage cells or ‘special cells’could be seen. The leaflets from plants grown in 400 mM NaCl,had larger numbers of intercellular air spaces; probably anindication of the beginning of tissue disorganization. A progressivedecrease in cell size of leaflets as salinity rose was alsodemonstrated. Prosopis tamarugo Phil., seedling, salinity, anatomical changes     

Understanding the Relationship between Cotton Fiber Properties and Non-Cellulosic Cell Wall Polysaccharides

A detailed knowledge of cell wall heterogeneity and complexity is crucial for understanding plant growth and development. One key challenge is to establish links between polysaccharide-rich cell walls and their phenotypic characteristics. It is of particular interest for some plant material, like cotton fibers, which are of both biological and industrial importance. To this end, we attempted to study cotton fiber characteristics together with glycan arrays using regression based approaches. Taking advantage of the comprehensive microarray polymer profiling technique (CoMPP), 32 cotton lines from different cotton species were studied. The glycan array was generated by sequential extraction of cell wall polysaccharides from mature cotton fibers and screening samples against eleven extensively characterized cell wall probes. Also, phenotypic characteristics of cotton fibers such as length, strength, elongation and micronaire were measured. The relationship between the two datasets was established in an integrative manner using linear regression methods. In the conducted analysis, we demonstrated the usefulness of regression based approaches in establishing a relationship between glycan measurements and phenotypic traits. In addition, the analysis also identified specific polysaccharides which may play a major role during fiber development for the final fiber characteristics. Three different regression methods identified a negative correlation between micronaire and the xyloglucan and homogalacturonan probes. Moreover, homogalacturonan and callose were shown to be significant predictors for fiber length. The role of these polysaccharides was already pointed out in previous cell wall elongation studies. Additional relationships were predicted for fiber strength and elongation which will need further experimental validation.     

Changes in Parenchyma Cells of Poplar Xylem during Transition from Growing to Wintering Stages

Ultrastructural changes in xylem parenchyma cells during transitionfrom growing to wintering stages were investigated. Changesin the fine structures of parenchyma cells in differentiatedxylem started in mid-August. At this time, dictyosomes werefrequently found and vesicles were abundant in the cells inwhich active formation of cellular structures took place. Thecytosol was filled with polysomes. In mid-September, the cytoplasmof the parenchyma cells gradually began to fill up with microbodies,and the endoplasmic reticulum cisternae had already startedto decrease. Dictyosomes and vesicles were still abundant atthis stage and microbody-associated vesicles could be seen,indicating participation of the vesicles in the formation ofmicrobodies at this stage. A direct structural connection withrespect to the biogenesis of the microbodies remained unclear.In the early stage, the microbodies showed a dense center surroundedby a less dense outer surface, and in the latter stage in November,the outer surface exhibited an increased accumulation of osmiophilicmaterials. There were few further changes in the overall patternof the fine structures until mid-winter. (Received July 2, 1987; Accepted November 30, 1987)