Molecular approaches to studying nutrient metabolism and function: an array of possibilities.

Genomics promises to revolutionize the study of nutrient function and requirements and, thereby, solidify the connection of this field to basic sciences, such as molecular genetics. In this short review, we address the general concepts and techniques used in high throughput measurements of gene expression. We also speculate on how these technologies can be used to further our understanding of basic metabolism and nutrient regulation of gene expression in developmental and pathological conditions.

Orchestrated transcription of key pathways in Arabidopsis by the circadian clock.

Like most organisms, plants have endogenous biological clocks that coordinate internal events with the external environment. We used high-density oligonucleotide microarrays to examine gene expression in Arabidopsis and found that 6% of the more than 8000 genes on the array exhibited circadian changes in steady-state messenger RNA levels. Clusters of circadian-regulated genes were found in pathways involved in plant responses to light and other key metabolic pathways. Computational analysis of cycling genes allowed the identification of a highly conserved promoter motif that we found to be required for circadian control of gene expression. Our study presents a comprehensive view of the temporal compartmentalization of physiological pathways by the circadian clock in a eukaryote.

Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog.

The toc1 mutation causes shortened circadian rhythms in light-grown Arabidopsis plants. Here, we report the same toc1 effect in the absence of light input to the clock. We also show that TOC1 controls photoperiodic flowering response through clock function. The TOC1 gene was isolated and found to encode a nuclear protein containing an atypical response regulator receiver domain and two motifs that suggest a role in transcriptional regulation: a basic motif conserved within the CONSTANS family of transcription factors and an acidic domain. TOC1 is itself circadianly regulated and participates in a feedback loop to control its own expression.

Fluorescent differential display identifies circadian clock-regulated genes in Arabidopsis thaliana.

Circadian rhythms in gene expression were first observed in plants more than 13 years ago, but the underlying mechanism controlling rhythmic gene expression is still not understood. The isolation of novel circadian clock-controlled genes (ccgs) is likely to provide new tools for studying circadian rhythms. Fluorescent differential display (FDD) was used to screen Arabidopsis thaliana mRNAs for cycling transcripts. Seventy PCR primer pairs were screened, and 17 different cycling bands were observed out of an estimated 10,500 bands screened. The identities of 10 bands were determined, and the rhythmic gene expression was confirmed using northern blot analysis. The 10 cycling bands represent 7 different genes, 6 of which are present in the databases and 1 that does not match anything in current databases. The rhythmic expression of the 7 genes is composed of four distinct phases of clock regulation. The results demonstrate that FDD can be used to isolate ccgs. The genes identified in this screen range from known A. thaliana ccgs, as well as genes shown to be clock controlled in other plant species, to a novel gene that may encode a pioneer protein. Further study of these ccgs is likely to increase our understanding of circadian-regulated gene expression.

Environmental and genetic effects on circadian clock-regulated gene expression in Arabidopsis.

Expression patterns of the cold-circadian rhythm-RNA binding (CCR) and chlorophyll a/b binding (CAB) protein genes have circadian rhythms with phases that are different from each other and are affected differently by cold (4 degrees C) treatment. Cycling of CCR and CAB RNA levels was observed in Arabidopsis seedlings grown for 5 days at 4 degrees C under a light/ dark photoperiod, although the cycling had reduced amplitude compared with normal growth conditions (20 degrees C). CCR RNA levels were elevated in the cold, whereas CAB RNA levels were reduced in the cold relative to levels in control seedlings. Cold pulses (4 degrees C for 12 or 20 hr) under continuous light affected the rhythms of CCR and CAB RNA levels in similar ways. The 12-hr cold pulse caused a 4-hr phase delay in both rhythms, whereas the 20-hr cold pulse resulted in a 12-hr phase delay in both rhythms. The timing of CAB expression 1 (toc1) mutation shortened the period of the CCR rhythm, matching previous results for the regulation of the CAB-luciferase (CAB-luc) transgene in this mutant. The results suggest that CCR and CAB share clock machinery but are regulated by downstream components that are affected differently by the cold. Also, the circadian clock regulating these genes in Arabidopsis has a cold-sensitive phase under continuous light conditions.

Molecular basis of alpha-methyltryptophan resistance in amt-1, a mutant of Arabidopsis thaliana with altered tryptophan metabolism.

A mutant of Arabidopsis thaliana, amt-1, was previously selected for resistance to growth inhibition by the tryptophan analog alpha-methyltryptophan. This mutant had elevated tryptophan levels and exhibited higher anthranilate synthase (AS) activity that showed increased resistance to feedback inhibition by tryptophan. In this study, extracts of the mutant callus exhibited higher AS activity than wild-type callus when assayed with either glutamine or ammonium sulfate as amino donor, thus suggesting that elevated AS activity in the mutant was due to an alteration in the alpha subunit of the enzyme. The mutant also showed cross-resistance to 5-methylanthranilate and 6-methylanthranilate and mapped to chromosome V at or close to ASA1 (a gene encoding the AS alpha subunit). ASA1 mRNA and protein levels were similar in mutant and wild-type leaf extracts. Levels of ASA1 mRNA and protein were also similar in callus cultures of mutant and wild type, although the levels in callus were higher than in leaf tissue. Sequencing of the ASA1 gene from amt-1 revealed a G to A transition relative to the wild-type gene that would result in the substitution of an asparagine residue in place of aspartic acid at position 341 in the predicted amino acid sequence of the ASA1 protein. The mutant allele in strain amt-1 has been renamed trp5-1.

Genes encoding glycine-rich Arabidopsis thaliana proteins with RNA-binding motifs are influenced by cold treatment and an endogenous circadian rhythm.

We have characterized the expression of two members of a class of Arabidopsis thaliana glycine-rich, putative RNA-binding proteins that we denote Ccr1 and Ccr2. Southern blot analysis indicates that Ccr1 and Ccr2 are members of a small gene family. Both Ccr1 and Ccr2 mRNA levels were influenced by a circadian rhythm that has an unusual phase for plants, with maximal accumulation at 6:00 PM and minimal accumulation at 10:00 AM. The level of CCR1 protein, however, remained relatively constant throughout the cycle. The transcript accumulation patterns of the Ccr1 and Ccr2 genes differed considerably from conditions that affect the expression of similar genes from maize, sorghum, and carrot. Levels of Ccr1 and Ccr2 mRNAs were unchanged in wounded plants, increased at least 4-fold in cold-stressed plants, and decreased 2- to 3-fold in abscisic acid-treated plants. Ccr1 transcript levels decreased in response to drought, whereas Ccr2 transcript levels increased under the same conditions. Based on the presence of additional Ccr transcripts in dark-grown plants, we propose that Ccr transcripts may be subjected to a light- or dark-mediated regulation.

Isolation and Characterization of a Mutant of Arabidopsis thaliana Resistant to alpha-Methyltryptophan.

Mutants of Arabidopsis thaliana have been selected for resistance to growth inhibition at the seedling stage by alpha-methyltryptophan (aMT). One mutant, amt-1 has been characterized in detail. The appearance and growth rate of the mutant in the absence of the inhibitor are similar to wild type, both as plants and callus. However, mutant plant growth is unaffected by 25 micromolar aMT and mutant callus growth by 50 micromolar aMT, concentrations that completely inhibit the growth of wild-type plants and callus, respectively. Tryptophan levels in mutant and wild-type plants are 24.3 +/- 2.7 and 4.7 +/- 1.2 micrograms per gram fresh weight, respectively, and in the corresponding callus 64.0 +/- 2.6 and 31.8 +/- 8.4 micrograms per gram fresh weight, respectively. Anthranilate synthase (AS) activity levels in crude extracts from whole plants are 3.09 +/- 0.54 nanomoles per milligram protein per hour in amt-1 and 1.32 +/- 0.21 nanomoles per milligram protein per hour in wild-type plants. In crude extracts from callus, anthranilate synthase levels are 11.54 +/- 2.05 nanomoles per milligram protein per hour and 7.74 +/- 1.58 in amt-1 and wild type, respectively. Enzyme extracts are inhibited by l-tryptophan; the concentrations required for 50% inhibition (I(50)) are 3.9 and 1.9 micromolar for amt-1 and for wild type, respectively. The mutation segregates as a single nuclear allele and shows incomplete dominance. The concomitant increases in both AS activity and its I(50) for tryptophan suggest that the mutation amt-1 either resides in one of the AS structural genes or causes increased expression of an AS isoform with an I(50) greater than the average for the entire extract.

Simple visual assay for determination of Pasteurella haemolytica cytotoxin neutralizing antibody titers in cattle sera.

A simple visual assay is described for determining the capacity of bovine serum to neutralize the cytotoxin produced by Pasteurella haemolytica serotype 1. The test was reproducible from day to day with different target cell populations and cytotoxin preparations. Cytotoxin neutralization titers obtained by the visual assay were comparable to those determined by the trypan blue exclusion and 51Cr-release methods. The visual assay was used to measure neutralization titers of bovine sera obtained from vaccination experiments and fractions of purified serum obtained by gel filtration. The major advantages of the visual assay over other assays are that it is rapid, inexpensive, and does not use radioisotopes. It also does not require specialized equipment, making it adaptable to most laboratories.

Serum antibodies to antigens derived from a saline extract of Pasteurella haemolytica: correlation with resistance to experimental bovine pneumonic pasteurellosis.

The serum antibody response was determined to 6 antigen groups (AG's) derived from a saline extract (SE) of Pasteurella haemolytica, serotype 1. Using an enzyme-linked immunosorbent assay, sera were analyzed from 65 calves that had been previously vaccinated with saline, the unfractionated SE, a bacterin, or live P. haemolytica. The serum antibody responses to the 6 AG's were correlated with resistance to an experimental transthoracic challenge with the organism. The antibody responses to AG's 1, 5, and 6 appeared to be potentially important in resistance to challenge. In the 3 experiments conducted, a significantly higher (p less than 0.05) increase in antibody was seen to AG's 1, 5, and 6 in calves vaccinated with live organisms compared to those vaccinated with the bacterin. A significant correlation (p less than 0.05) was seen between high antibody to AG 1 and resistance to challenge in all 3 experiments. In 2 of the 3 experiments, a significant correlation (p less than 0.05) was seen among high antibody titers to AG's 5 and 6 and resistance, whereas in 1 experiment the correlation was significant (p less than 0.05) between antibody to AG 4 and resistance. A rise in antibody to AG's 2 and 3 was seen only in calves vaccinated with SE. Because AG's 1, 5, and 6 are higher in carbohydrate than the other AG's, this suggests that antibody to polysaccharide antigens may be important to resistance. Other potentially protective antigens of P. haemolytica are discussed.