Estimating the Growth Rate of Slowly Growing Marine Bacteria from RNA Content

In past studies of enteric bacteria such as Escherichia coli, various measures of cellular RNA content have been shown to be strongly correlated with growth rate. We examined this correlation for four marine bacterial isolates. Isolates were grown in chemostats at four or five dilution rates, yielding growth rates that spanned the range typically determined for marine bacterial communities in nature (μ = 0.01 to 0.25 h^-1). All measures of RNA content (RNA cell^-1, RNA:biovolume ratio, RNA:DNA ratio, RNA:DNA:biovolume ratio) were significantly different among isolates. Normalizing RNA content to cell volume substantially reduced, but did not eliminate, these differences. On average, the correlation between μ and the RNA:DNA ratio accounted for 94% of variance when isolates were considered individually. For data pooled across isolates (analogous to an average measurement for a community), the ratio of RNA:DNA μm^-3 (cell volume) accounted for nearly half of variance in μ (r² = 0.47). The maximum RNA:DNA ratio for each isolate was extrapolated from regressions. The regression of (RNA:DNA)/(RNA:DNA)_max on μ was highly significant (r² = 0.76 for data pooled across four isolates) and virtually identical for three of the four isolates, perhaps reflecting an underlying common relationship between RNA content and growth rate. The dissimilar isolate was the only one derived from sediment. Cellular RNA content is likely to be a useful predictor of growth rate for slowly growing marine bacteria but in practice may be most successful when applied at the level of individual species.     

GEOTAXIS/PHOTOTAXIS AND BIOCHEMICAL PATTERNS IN HETEROCAPSA (=CACHONINA) ILLDEFINA (DINOPHYCEAE) DURING DIEL VERTICAL MIGRATIONS

Two separate experiments with Heterocapsa (= Cachonina ) illdefina Herman et Sweeney, one with and the other without water volume replacement, were performed in a 250-L laboratory mesocosm (45-cm diameter × 150-cm height) to examine how diel vertical migration (DVM) relates to taxis sign and strength and to cellular biochemical state. Although only the cell population grown with water volume replacement maintained a division per day over the course of the experiment, periodic measurements during both experiments demonstrated that cells aggregating at the surface during the light period generally were deficient in all measured biochemical constituents compared to cells obtained from a midcolumn depth. More specifically, H. illdefina cells that aggregated at the surface during the light period in both experiments exhibited weakened positive geotaxis but strengthened positive phototaxis and were very deficient in lipid and free amino acid compared to midcolumn cells. Cells sampled at midcolumn during the light period exhibited similar but weaker taxes changes compared to surface samples, and geotaxis strength was inversely correlated with cell diameter, cellular DNA and protein content, and RNA/DNA ratio. In comparison, published data on Gymnodinium breve Davis, a harmful algal bloom species, showed that cells aggregating at the surface during the light period generally exhibited weakened negative geotaxis and strengthened positive phototaxis and were very deficient in lipid and chl a compared to midcolumn cells. Although the persistent tendency toward negative geotaxis was weaker in midcolumn subpopulations throughout the day, its strength was inversely correlated with cell diameter and cellular lipid content. The combined results for both species support a revised conceptual model of optimized DVM in autotrophic marine dinoflagellates incorporating generalized expressions of taxis and biochemical state of individual cells.     

Changes in amount and synthesis of poly(A)- and poly(A)+ RNA in growing and resting cultures of Tetrahymena

This investigation deals both qualitatively and quantitatively with the changes of RNA content and synthesis during the culture growth cycle of Tetrahymena. Affinity chromatography with an oligo(dT) column was used to separate poly(A)+ RNA from total RNA. The rates of synthesis of poly(A)- and poly(A)+ RNA were determined in terms of the incorporation of [5-3H]uridine. During the log phase, the cellular RNA and protein contents decreased steadily, whereas during the resting stage, both were constant. The extents of decrease of both fractions of RNA were essentially the same (54.4% and 50.6% for total and poly(A)+ RNA, respectively). Therefore, the relative contents of poly(A)+ RNA was constant from the beginning of the log to the resting stage (4.58%). The decrease in protein content, however, amounted to only 24.8%. Theoretically, a change in the age distribution during culture growth would cause a lower content of both fractions of RNA. The extents of the decrease in the rate of synthesis of both fractions were the same (75% and 79% for poly(A)- and poly(A)+ RNA, respectively). However, this reduction is so large that it cannot be solely the result of a shift of the age distribution of the cell population.     

Correlation between cell enlargement and nucleic acid and protein content of HeLa cells in unbalanced growth produced by inhibitors of DNA synthesis

HeLa cells in monolayer cultures were treated with the following inhibitors of DNA synthesis: mitomycin C, nitrogen mustard, fluorodeoxyuridine, hydroxyurea, arabinofuranosylcytosine and high concentrations of thymidine. The concentration of each inhibitor used was, in most cases, just sufficient to arrest cell multiplication and all produced unbalanced growth in the sense that the synthesis of RNA and protein were only partially inhibited while DNA synthesis stopped. This resulted in approximately 100% increases in RNA and protein content per cell in 48 hours and, since cell volume also increased by 100% during this time, the concentration of RNA and protein per unit cell volume remained constant. It was concluded that cell protein content may be used as an accurate index of variation in cell size in HeLa cells treated with inhibitors of DNA synthesis.     

Correlation between cell cycle duration and RNA content.

The metachromatic fluorochrome acridine orange was used to differentially stain DNA and RNA in Chinese hamster ovary (CHO) cells and in mitogen-stimulated human lymphocytes during their progression through the cell cycle. Green and red fluorescence of individual cells, representing cellular DNA and RNA, respectively, was measured by flow cytometry. CHO cells were synchronized by selective detachment at mitosis. Their rate of progression through G1 and subsequently through S phase correlated with the content of stainable RNA. The mean duration of the G1 phase was 5.2 hours for cells with high RNA content (highest 25 percentile population) and 8.1 hours for cells with low RNA (lowest 25 percentile). The duration of S phase was 5.9 and 7.5 hours for high- and low-RNA, 25 percentile subpopulations, respectively. Lymphocytes synchronized at the G1/S boundary by hydroxyurea or 5-fluorodeoxyuridine showed extremely high intercellular variation with respect to content of stainable RNA. After release from the block they traversed S phase at rates linearly proportional to the content of stainable RNA. The duration of S phase was five hours for cells with high RNA-, six to nine hours for cells with moderate RNA- and up to 27 hours for cells with minimal RNA-content. The data suggest that the rate of progression through the cell cycle of individual cells within a population may be correlated with the number of ribosomes per cell.     

Mitochondrial development during Drosophila oogenesis: distribution, density and in situ RNA hybridizations.

The changes in distribution and density of mitochondria and the level of mitochondrial RNA during Drosophila oogenesis were studied simultaneously in the 3 cell types ie follicle cells, nurse cells and oocyte, making up the egg chamber. Up to stage 6, mitochondrial density (mitochondrial and cellular areas ratio) was elevated and increased similarly in both follicle and nurse cells. Thereafter the mitochondrial density of follicle cells continued to increase and that of the nurse cells declined markedly while the nurse cell mitochondria assembled in dense groups and decreased in size. This can be related to a transfer of nurse cell cytoplasm, including mitochondria, to the oocyte. In the oocyte from stage 4 to stage 7 we observed a significant decrease of the mitochondrial density due to the absence of mitochondrial biogenesis. Then the cytoplasm transfer caused mitochondrial density to increase up to the level found in the nurse cells at the end of oogenesis. The mature oocyte contains enough mitochondria to supply 15,000 somatic cells. Our results strongly suggest that the variations in size, distribution and density of mitochondria relate to the particular energetic requirements of the different cell types during the first half of oogenesis. Later they relate to the developmental requirements of the nurse cells and the oocyte, in particular the storage of mitochondria in the oocyte. The level of mitochondrial RNA was studied through in situ hybridization. Throughout oogenesis the follicle and nurse cell RNA evolved similarly. Up to stage 9, there was no change in RNA densities in these cells, suggesting a correlation with the cell volume and/or the nuclear DNA content. Thereafter the cellular RNA concentration declined rapidly. In the oocyte the RNA concentration evolved differently especially from stage 10 to the end, the RNA density being stabilized. This can be related to the injection of nurse cell mitochondria, followed by their assignment to reserve status. Our results suggest that the mt RNA density is under extramitochondrial control mechanisms.     

Synthesis of Protein, Ribonucleic Acid, and Ribosomes by Individual Bacterial Cells in Balanced Growth

Relative rates of protein synthesis in individual cells were determined by allowing random populations to incorporate tritiated leucine for very short periods (pulses) and then examining autoradiographs of these cells to assess the amount of incorporation (grains per cell) as a function of cell size. Relative rates of ribonucleic acid (RNA) synthesis were determined in the same way by using tritiated uracil. Unless the uracil pulse was very short (less than 1/20 generation), the RNA labeled during the pulse was predominantly ribosomal. The rate of protein synthesis in individual cells is directly proportional to cell size. The rate of RNA synthesis also increases linearly with size in larger cells, but there appears to be a slight delay in RNA synthesis immediately after cell division. Total cellular content of protein, RNA, and ribosomes is directly proportional to cell size. Thus, we conclude that, in individual cells during the cell cycle (i) the average rate of protein synthesis per ribosome is constant and (ii) the increase in macromolecular mass of the cell is exponential with age.     

Cytodifferentiation of the chick pancreas. 3. The content and synthesis of ribonucleic acid and proteins in developing acinar cells

The content and synthesis of ribonucleic acid (RNA) and protein was studied by microphotometry and autoradiography in the developing pancreatic acinar cells of White Leghorn chick embryos. These findings were correlated with previously reported changes in ultrastructural components. Shortly before or concomitant with zymogen granulation, RNA synthesis increased, in association with increases in the amount of nucleolar and cytoplasmic protein. The cytoplasmic fraction was transitory, whereas the accumulated nucleolar protein was maintained and was soon followed by an increase in nucleolar RNA. Concomitantly, a decrease in chromosomal RNA was observed, with the total amount of nuclear RNA staying constant. When zymogen first appeared, nucleoli were greatly enlarged due to large amounts of RNA and protein; total cellular RNA and protein had decreased slightly, in association with a decrease in cell volume. Subsequent development presented smaller nucleoli with decreased amounts of RNA and protein. Total cellular RNA increased due to its accumulation in the cytoplasm, probably as ribosomes. The accumulation of zymogen and the enlargement of other cellular structures contributed to an increase in total cellular protein. Prior to hatching, total cell RNA and protein decreased in amount, probably due to a reduction in cell volume through cell division.     

RNA-Induced Interference with Animal Virus Infection

Some RNAs, including both single- and double-stranded RNAs, when incubated with chick embryo cell culture induce cellular resistance against viruses. Evidence was now obtained indicating that the induction of cellular resistance by RNA depends on the cellular metabolic activity, especially on the synthesis of cellular RNA and protein. Thus, inhibitors of RNA and protein synthesis, actinomycin D and cycloheximide, were found to inhibit the development of an antiviral state when added before, or during the relatively early period of, incubation of the cells with RNA. In the course of induction of cellular resistance, three stages may be distinguished, the priming stage, the developing stage, and the established resistant stage.     

The ratio of RNA to total nucleic acid content as a quantitative measure of unbalanced cell growth

Use of the metachromatic dye, acridine orange, to stain cells in suspension for flow cytometry allows for the simultaneous measurement of DNA and RNA content in individual cells. The relative RNA content as a function of total cellular nucleic acid content [alpha r = RNA/(RNA + DNA)] is a constant value, characteristic for particular cell lines during their exponential growth under optimal conditions. This ratio can be estimated for the G1A, G1B, S, and G2 + M cell cycle compartments. Changes in growth rate or the addition of antitumor drugs induces characteristic changes in the ratio either evenly throughout or at a particular phase of the cell cycle. Under such conditions, measurement of cellular DNA and RNA content provides a sensitive assay of any deviation from balanced cell growth. Unbalanced growth caused by suboptimal culture conditions or as a result of incubation with various antitumor agents is illustrated. Examples of unbalanced growth which are not correlated with cell viability as measured by cell clonogenicity are discussed.     

Measles virus infection of B lymphocytes permits cellular activation but blocks progression through the cell cycle.

Measles virus infection of unstimulated B lymphocytes suppresses both proliferation and differentiation into immunoglobulin-secreting cells. However, mitogenic stimulation of these infected cells results in cell volume enlargement, rapid RNA synthesis, and the expression of cell surface activation antigens 4F2, HLA-DS, and transferrin receptor. The cellular genes c-myc and histone 2B are induced during early G1 and S phase of the cell cycle, respectively, and viral RNA synthesis can be detected during this interval. However, total RNA synthesis is decreased at 48 h after stimulation, and the histone 2B RNA steady-state level at 48 h is fivefold less than that in uninfected cells. This sequence of events defines an arrest in the G1 phase of the cell cycle in measles virus-infected B cells.     

Bacterial Growth on Surfaces: Automated Image Analysis for Quantification of Growth Rate-Related Parameters

A fast routine method for estimating bacterial cell growth rates by using the metachromatic dye acridine orange is described. The method allows simultaneous estimates of cellular RNA and DNA contents of single cells. Acridine orange staining can be used as a nonspecific supplement to quantitative species-specific hybridizations with fluorescence-labelled ribosomal probes to estimate the single-cell concentration of RNA. By automated analysis of digitized images of stained cells, we determined four independent growth rate-related parameters: cellular RNA and DNA contents, cell volume, and the frequency of dividing cells in a cell population. These parameters were used to compare physiological states of liquid-suspended and surface-growing Pseudomonas putida KT2442 in chemostat cultures. The major finding is that the correlation between substrate availability and cellular growth rate found for the free-living cells was not observed for the surface-bound cells; in contrast, the data indicate an almost constant growth rate for attached cells which was independent of the dilution rate in the chemostat.     

Nucleic Acid, Protein, and Starch Synthesis in Developing Cotyledons of Pisum arvense L.

During the cell-division period of cotyledon development inPisum arvense L. cell volume increases slightly but nuclearvolume shows little variation and the DNA content remains atthe 2C to 4C level. During the main period of cell expansionthere is a close correlation between cell volume, nuclear volume,and nuclear DNA content, the nuclei of the largest storage cellsfinally attaining the 64C level. The rate of RNA synthesis increasesseveral days after the increase in DNA has begun and at thesame time accumulation of reserve protein and starch begins.RNA and starch synthesis apparently cease some time before maturationbut protein synthesis continues until the seeds are ripe. Cotyledondevelopment was found to comprise two distinct phases: an initialphase of cell division and differentiation during which DNA,RNA, and protein per unit volume of cell decline; and a phaseof reserve accumulation in which DNA per unit volume of cellremains constant but RNA and protein per unit volume increase,starch synthesis is initiated, and all the cotyledon cells assumethe properties of storage cells.     

Mitochondrial development during Drosophila oogenesis: distribution,density and in situ RNA hybridizations

The changes in distribution and density of mitochondria and the level of mitochondrial RNA during Drosophila oogenesis were studied simultaneously in the 3 cell types ie follicle cells, nurse cells and oocyte, making up the egg chamber. Up to stage 6, mitochondrial density (mitochondrial and cellular areas ratio) was elevated and increased similarly in both follicle and nurse cells. Thereafter the mitochondrial density of follicle cells continued to increase and that of the nurse cells declined markedly while the nurse cell mitochondria assembled in dense groups and decreased in size. This can be related to a transfer of nurse cell cytoplasm, including mitochondria, to the oocyte. In the oocyte from stage 4 to stage 7 we observed a significant decrease of the mitochondrial density due to the absence of mitochondrial biogenesis. Then the cytoplasm transfer caused mitochondrial density to increase up to the level found in the nurse cells at the end of oogenesis. The mature oocyte contains enough mitochondria to supply 15 000 somatic cells. Our results strongly suggest that the variations in size, distribution and density of mitochondria relate to the particular energetic requirements of the different cell types during the first half of oogenesis. Later they relate to the developmental requirements of the nurse cells and the oocyte, in particular the storage of mitochondria in the oocyte. The level of mitochondrial RNA was studied through in situ hybridization. Throughout oogenesis the follicle and nurse cell RNA evolved similarly. Up to stage 9, there was no change in RNA densities in these cells, suggesting a correlation with the cell volume and/or the nuclear DNA content. Thereafter the cellular RNA concentration declined rapidly. In the oocyte the RNA concentration evolved differently especially from stage 10 to the end, the RNA density being stabilized. This can be related to the injection of nurse cell mitochondria, followed by their assignment to reserve status. Our results suggest that the mt RNA density is under extramitochondrial control mechanisms.     

Phage formation in Staphylococcus muscae cultures; nucleic acid synthesis during virus formation

1. The total nucleic acid synthesized by normal and by infected S. muscae suspensions is approximately the same. This is true for either lag phase cells or log phase cells. 2. The amount of nucleic acid synthesized per cell in normal cultures increases during the lag period and remains fairly constant during log growth. 3. The amount of nucleic acid synthesized per cell by infected cells increases during the whole course of the infection. 4. Infected cells synthesize less RNA and more DNA than normal cells. The ratio of RNA/DNA is larger in lag phase cells than in log phase cells. 5. Normal cells release neither ribonucleic acid nor desoxyribonucleic acid into the medium. 6. Infected cells release both ribonucleic acid and desoxyribonucleic acid into the medium. The time and extent of release depend upon the physiological state of the cells. 7. Infected lag phase cells may or may not show an increased RNA content. They release RNA, but not DNA, into the medium well before observable cellular lysis and before any virus is liberated. At virus liberation, the cell RNA content falls to a value below that initially present, while DNA, which increased during infection falls to approximately the original value. 8. Infected log cells show a continuous loss of cell RNA and a loss of DNA a short time after infection. At the time of virus liberation the cell RNA value is well below that initially present and the cells begin to lyse.     

Cell-to-Cell Diversity in a Synchronized Chlamydomonas Culture As Revealed by Single-Cell Analyses

In a synchronized photoautotrophic culture of Chlamydomonas reinhardtii, cell size, cell number, and the averaged starch content were determined throughout the light-dark cycle. For single-cell analyses, the relative cellular starch was quantified by measuring the second harmonic generation (SHG). In destained cells, amylopectin essentially represents the only biophotonic structure. As revealed by various validation procedures, SHG signal intensities are a reliable relative measure of the cellular starch content. During photosynthesis-driven starch biosynthesis, synchronized Chlamydomonas cells possess an unexpected cell-to-cell diversity both in size and starch content, but the starch-related heterogeneity largely exceeds that of size. The cellular volume, starch content, and amount of starch/cell volume obey lognormal distributions. Starch degradation was initiated by inhibiting the photosynthetic electron transport in illuminated cells or by darkening. Under both conditions, the averaged rate of starch degradation is almost constant, but it is higher in illuminated than in darkened cells. At the single-cell level, rates of starch degradation largely differ but are unrelated to the initial cellular starch content. A rate equation describing the cellular starch degradation is presented. SHG-based three-dimensional reconstructions of Chlamydomonas cells containing starch granules are shown.