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Journal of Bacteriology, April 2004, p. 2340-2345, Vol. 186, No. 8
0021-9193/04/$08.00+0 DOI: 10.1128/JB.186.8.2340-2345.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824,1 Department of Earth Sciences, University of Southern California, Los Angeles, California 90089-07402
Received 20 June 2003/ Accepted 8 January 2004
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Of major concern to organisms living over a wide range of temperatures is the fact that reaction rates decrease exponentially as temperature decreases. This also holds for bacterial growth rates (essentially a collection of chemical reactions). However, when bacterial growth rate (µ) is examined on an Arrhenius plot (log µ versus 1/T), two linear domains often appear below Topt. The point at which the slope changes is designated the critical temperature (Tcritical). The existence of Tcritical has been reported for eurypsychrophiles, mesophiles, and thermophiles (5, 6, 9, 12, 13, 15, 22, 35). The lack of Tcritical reports for stenopsychrophiles is probably because their growth rates have not been systematically examined at sufficiently low temperatures. It is hypothesized that Tcritical exists as a result of increased energy demands, the synthesis of stress proteins, and/or the use of alternate metabolic pathways at low temperatures (6, 10, 12).
Understanding the basis of Tcritical is important because much of the earth's surface is permanently at or below 4°C and the microorganisms isolated from permanently cold ecosystems (e.g., sea ice, glacial ice, the deep sea, and permafrost) generally have Topt values much greater than in situ temperatures (Tin situ) (2, 18, 23, 29, 31). Furthermore, eurypsychrophiles are isolated more frequently from low-temperature environments than are stenopsychrophiles (29, 37). Stenopsychrophiles are more adapted to low temperatures than eurypsychrophiles and subsequently have faster growth rates at 0°C (13, 29). In addition, stenopsychrophiles compensate for low growth rates at Tin situ by having growth yields that peak around Tin situ or remain constant from Topt to Tin situ (13, 15, 19). Unfortunately for eurypsychrophiles, not only is Topt greater than Tin situ but Tcritical is also greater than Tin situ.
Given that eurypsychrophiles predominate in low-temperature environments, where Tin situ is lower than Tcritical, the question arises as to how eurypsychrophiles function at temperatures below Tcritical and Topt. Thus, we have examined how the rate of growth of P. cryopegella, rates of DNA, RNA, and protein synthesis, and growth yield are affected by temperature. Here, we report the Tcritical of P. cryopegella (4°C) and its relation to macromolecular synthesis and growth yield. While RNA, protein, and DNA synthesis rates decreased exponentially with decreasing temperatures, on a per-cell-division basis, RNA and protein synthesis reached a minimum at Tcritical and DNA synthesis was constant over the entire temperature range. Growth yield peaked at about Tcritical, with further decreases in temperature resulting in much reduced yields. The correlation of high growth yields with low RNA synthesis requirements per cell division was confirmed via examination of the mesophile Shewanella oneidensis MR-1.
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For macromolecular synthesis experiments conducted at temperatures at or above 0°C, P. cryopegella or S. oneidensis was first grown at the experimental temperature for 1 to 7 days, diluted (1:10) into 18 ml of fresh R3 in 30-ml polycarbonate straight-sided jars (Nalgene), and incubated for an additional 1.5 to 24 h prior to the addition of [3H]leucine or [3H]adenine. For experiments conducted at -4 and -7°C, P. cryopegella was grown overnight at 22°C, diluted (1:20) into fresh R3, and incubated for an additional 11 days at -4°C or 6 days at -7°C. Prior to the addition of [3H]leucine or [3H]adenine, 4-ml subsamples were removed to determine optical density at 600 nm and cell numbers by dilution plating. For killed controls, 0.16 g of trichloroacetic acid (TCA) was added.
Growth yield. Triplicate cultures of P. cryopegella were grown in 50 ml of LB3 (10 g of glucose, 30 g of NaCl, and 5 g of yeast extract [all per liter] [pH 7.0]) in 250-ml flasks at 20, 16, 10, 4, 0, -4, and -10 °C with shaking at 100 rpm. The flasks were inoculated with a loopful of cells, and cultures were collected during exponential phase. Cultures grown at 0, -4, and -10°C were inoculated with 5 ml of an overnight culture grown at 16°C and incubated for 5, 6, and 20 days, respectively. Cell weights and glucose concentrations of inocula were also measured. Cells were collected by centrifugation for 10 min at 10,000 x g and 4°C. Cell pellets were washed with 5 ml of phosphate buffer, recollected by centrifugation, resuspended in 0.5 ml of phosphate buffer, transferred to preweighed Al trays, dried at 65°C for 3 days, and weighed. Supernatants were stored at -20°C and passed through 0.2-µm-pore-size filters prior to analysis using Sigma's glucose (GO) assay kit (GAGO-20).
DNA and RNA synthesis rates. [3H]adenine incorporation rates into DNA and RNA were determined by standard procedures with minor modifications (16). Briefly, [2,8-3H]adenine (specific activity, 24.2 Ci/mmol; Perkin-Elmer) was added to a final concentration of 30 nM and samples were incubated for at least 10% of the expected doubling time at the experimental temperature. Subsamples were taken in duplicate at six or seven time points within this incubation period. At the time points, 1 ml of culture was filtered through a 25-mm-diameter Whatman GF/F filter in a glass filter tower, placed into a 1.5-ml Eppendorf tube, and stored at -80°C. Filters were removed from the freezer, and 1 ml of ice-cold 5% TCA, 1 mg of reagent RNA (baker's yeast; Sigma), and 1 mg of DNA (calf thymus; Sigma) were added. Samples were mixed thoroughly, incubated on ice for 1 h, and spun at 12,000 x g for 1 min, and the supernatant was discarded. Filters were washed three times with 1 ml of ice-cold 5% TCA and three times with 1 ml of ice-cold 95% ethanol. Residual ethanol was evaporated by gentle heating. Filters were mixed with 1 ml of 1 M NaOH, incubated at 37°C for 1 h, incubated on ice for 15 min, mixed with 0.25 ml of 9 M HCl-100% TCA-H2O (2:1:1), incubated on ice for 15 min, and spun at 12,000 x g for 1 min. For [3H]RNA analysis, 0.625 ml of supernatant was transferred to a clean scintillation vial while the remaining supernatant was discarded. Subsequently, filters were washed two times with 1 ml of ice-cold 5% TCA and two times with ice-cold 95% ethanol. Residual ethanol was evaporated by gentle heating. Filters were mixed with 0.5 ml of 5% TCA, incubated at 95 to 100°C for 30 min, cooled on ice, mixed with 0.5 ml of 1 M NaOH, and spun at 12,000 x g for 1 min. For [3H]DNA analysis, 0.5 ml of supernatant was transferred to a clean scintillation vial containing 0.5 ml of 2 M HCl. Five milliliters of BetaMax Scintillation cocktail (ICN) was added to vials followed by analysis in a Beckman LS6000 scintillation counter for 3H.
Protein synthesis rates. [3H]leucine incorporation rates were determined by standard procedures (17). Briefly, [3,4,5-3H(N)]leucine (specific activity, 170 Ci/mmol; Perkin-Elmer) was added to a final concentration of 4.2 nM. Samples were incubated and subsampled as above. At time points, 1 ml of culture was filtered through a 25-mm-diameter Whatman GF/F filter in a glass filter tower, rinsed twice with 3 ml of ice-cold 5% TCA, and rinsed twice with 3 ml of ice-cold 80% ethanol. Filters were placed into clean scintillation vials and air dried. Five milliliters of scintillation cocktail was added to the vials, incubated at room temperature for 2 days to maximize dispersion into the cocktail, and analyzed in a Beckman LS6000 scintillation counter as described above.
Calculations and statistical analyses. Specific growth rates (µ) were calculated by determining the slope of the straight-line portion of exponential growth (on a semilog plot). At least six time points over approximately three doublings were used to determine the slope of the line of best fit. The minimum acceptable r2 value of the lines was 0.8 (average r2 = 0.959). The average growth rate and standard deviation for each temperature were calculated by standard methods. For normalization purposes (see below), the growth rate at -7°C for P. cryopegella was determined from the line of best fit (µ = 0.308 e0.271 T, r2 = 0.987) for data from 4 to -10°C.
Growth yield was calculated as follows: YGlc = (mcells x MWGlc)/[V x ([Glc]initial- [Glc]final)], where mcells is the grams (dry weight) of cells produced, MWGlc is the molecular weight of glucose in grams/mole, [Glc] is the concentration of glucose in grams/liter, and V is the volume of the culture in liters. The average growth yield and standard deviation at each temperature were calculated by standard methods. Standard t tests were performed to verify the significance of differences in YGlc between temperatures.
Synthesis rates (k) were calculated from the linear portion of the 3H uptake versus time curve (duplicate samples minus killed controls). The slope and r2 value for these lines were determined (r2 ranged from 0.56 to 0.99, with an average of 0.86, for 21 slopes). The standard error of each slope (SEb) was calculated as follows: SEb = SEY|X/
SSXX, where SEY|X is the standard error of the regression and SSXX is the sum of squares of X. The standard error of regression, SEY|X, is equal to
[(SSYY - b x SSXY)/(n - 2)], where b is the slope, SSYY is the sum of squares of Y, and SSXY is the sum of the cross-products of X and Y. The sum of squares of X is equal to
(analogous calculation for SSYY). The sum of the cross-products of X and Y is equal to
.
Normalized rates, kN, were calculated as follows: kN = k/µ, where k is the 3H uptake rate in zeptomoles/cell/day and µ is the specific growth rate in divisions/day. The standard deviation of the normalized rate was calculated as follows:
= kN x
[(SEb/k)2 + (
µ/µ)2], where SEb is the standard error of k and
µ is the standard deviation of the growth rate. Standard t tests were performed to verify the significance of differences in kN between temperatures.
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FIG. 1. Temperature dependence of P. cryopegella growth rate. Each point represents the average of two to four replicates. Standard deviations are shown. Note that the y axis is a log scale, and lines of best fit are shown.
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FIG. 2. Temperature dependence of P. cryopegella growth yield. Each point represents the average of triplicate samples (except for -10 and -4°C, which represent two and one sample, respectively). Standard deviations are shown.
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FIG. 3. (A) Temperature dependence of P. cryopegella macromolecular synthesis rates. Each point represents the slope of the linear portion of the tritium uptake versus time curve for two samples minus killed controls. Standard errors of the slopes are shown. Note that the y axis is a log scale, and lines of best fit are shown. (B) Temperature dependence of P. cryopegella normalized macromolecular synthesis rates. (1 zmol = 10-21 mol.)
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Macromolecular synthesis rates and yield of S. oneidensis MR-1. For comparison, the DNA and RNA synthesis rates (kDNA and kRNA, respectively) and growth rates (µ) of the mesophilic S. oneidensis MR-1 were measured from 4 to 22°C (Fig. 4A). Both the DNA synthesis rate and growth rate generally followed the Arrhenius relationship (kDNA = 24.8 e0.083 T; r2 = 0.925; and µ = 0.690 e0.087 T; r2 = 0.971) Normalized respiration rates indicated that Tcritical was about 12°C for S. oneidensis (data not shown); however, no obvious deviations from the linear relationship for kDNA and µ occurred at Tcritical. Below 18°C, RNA synthesis rates remained constant with temperature.
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FIG. 4. Analogous data for the mesophile S. oneidensis MR-1. (A) Temperature dependence of macromolecular synthesis and growth rates. Each point represents the slope of the linear portion of the tritium uptake versus time curve for two samples minus killed controls (for growth rate, each point represents the average of two to four samples). Lines of best fit are shown for DNA synthesis and growth rates. The standard error (synthesis rates) or standard deviation (growth rate) is shown. Note that the y axis is a log scale. (1 zmol = 10-21 mol.) (B) Temperature dependence of normalized macromolecular synthesis rates. (C) Yield versus temperature. Cell yield was measured as the number of cells present at the beginning of stationary phase at each temperature. Each point represents the average of at least three samples; standard deviations are shown.
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The yield of S. oneidensis MR-1 was estimated as the number of cells present at early stationary phase during growth in LB at various temperatures (Fig. 4C). Yield was highest and approximately constant from 14 to 22°C; t tests showed no significant difference between cell yields at these temperatures (P > 0.15). Below 14°C, yield decreased significantly (P < 0.05) as temperature decreased.
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We examined the temperature dependence of growth rate and DNA, RNA, and protein synthesis rates to elucidate the basis of Tcritical. In P. cryopegella, the temperature dependence of both DNA synthesis rate and growth rate changed at Tcritical. The slopes for both linear domains of kDNA and growth rate were similar, suggesting that these two processes are tightly coupled. It is not likely that a temperature-dependent change in the DNA replication machinery caused Tcritical because no such change has ever been reported, nor has the control of growth rate by DNA synthesis. Cell reproduction probably slowed for other reasons, causing the growth rate and DNA synthesis rate to be regulated accordingly. The temperature dependence of protein and RNA synthesis rates in P. cryopegella did not change at Tcritical, indicating that its ribosomes and RNA polymerases remained functional at temperatures below Tcritical, as has been demonstrated for other psychrophiles (32-34). (Note: protein and RNA elongation rates are temperature dependent, while the numbers of ribosomes and RNA polymerases remain constant with temperature [9, 12, 30]). In contrast, when grown at the same temperature but at different growth rates, bacteria alter their protein synthetic capacity by changing the number of ribosomes (21, 24).) Genotypic adaptation of ribosomes to low temperatures has been demonstrated in cold-tolerant strains of Bacillus cereus that were shown to substitute A and T for G and C, when compared to mesophilic strains (26). Conversely, in mesophiles the temperature dependence of protein synthesis rates changes at Tcritical, reflecting the inability of mesophilic ribosomes to function at low temperatures (7, 9, 32-34).
Subsequently, we normalized synthesis rates in order to reveal temperature-dependent processes that were masked by the primary effect of decreasing temperature (exponential decrease in reaction rates). Normalized rates allowed examination of synthesis requirements on a per-cell-division basis rather than time. There was no significant change in kDNAN. with temperature in P. cryopegella, because the same DNA synthesis requirement exists for each cell division. Specifically, one genome must be synthesized per cell division. Both kRNAN and kPN were at a minimum at Tcritical, indicating that cell reproduction required the least amount of RNA and protein synthesis at this temperature. Conversely, cell reproduction at temperatures above and below Tcritical required the synthesis of additional RNA and proteins (or higher levels of the same RNA and proteins). Indeed, temperatures of 10°C and below induced the expression of both cold acclimation proteins (CAPs) and cold shock proteins (CSPs) in psychrophilic bacteria (7, 8, 14, 27, 36). Furthermore, as temperature decreased, more CAPs and CSPs are produced and expressed at higher levels (14, 27, 36). To date, cold response studies have examined 5°C temperature increments and found that expression of CAPs and CSPs changed at all increments (14, 27, 36). This study examined 3 to 6°C increments, and statistically significant changes in RNA and protein synthesis rates were seen between most of the increments. However, how these data relate to production of CAPs and CSPs is unclear. Above Tcritical, the kRNANand kPN may increase due to the production of additional proteins and/or increased protein turnover caused by higher rates of denaturation and degradation (9, 11, 25, 38). It is striking that cell reproduction required the least amount of RNA and protein synthesis at Tcritical and that growth yield peaked at Tcritical.
While this study focused on Tcritical in psychrophiles, the synthesis rates, normalized rates, and growth yield were examined in the mesophile S. oneidensis MR-1 for comparison. The growth yield of S. oneidensis MR-1 displayed thermal characteristics typical of mesophiles (yield peaked at high temperatures). Likewise, DNA synthesis rates and growth rates decreased with T according to the Arrhenius relationship. Unlike most mesophiles however, S. oneidensis MR-1 maintained RNA synthesis rates from 18 to 4°C. Regardless of this ability, the normalized RNA synthesis rate of S. oneidensis MR-1 also changed at Tcritical, as seen in P. cryopegella. In addition, minimal normalized RNA synthesis rates corresponded to temperatures with the highest yields. Therefore, S. oneidensis MR-1 grew most efficiently (that is, it minimized RNA synthesis requirements for cell division) at temperatures above Tcritical, while P. cryopegella did so only at Tcritical.
In summary, the most beneficial survival strategy for psychrophiles may be to maximize growth yield, not growth rates, at low temperatures. P. cryopegella accomplished this by streamlining growth processes (cell reproduction required the synthesis of the least amount of protein and RNA) at a fairly low temperature (4°C, Tcritical). In addition, we demonstrated that at Tcritical growth of P. cryopegella was separated into two domains and, previously, that below Tcritical the respiration requirement for cell reproduction increased dramatically (4). Identifying the cell processes that lead to Tcritical is vital to understanding low-temperature growth. Prior to this study, no basic mechanisms involved in maximizing or maintaining growth yields at low temperatures had been identified. This type of growth strategy may be an essential part of being able to live over a wide range of temperatures. While this study presented one approach to define the basis of Tcritical, it remains to be determined whether or not Tcritical is a pivotal temperature in psychrophiles with respect to global stress response.
Thanks to M. Thomashow and J. Tiedje for facilitating the completion of experiments at Michigan State University that were begun at the University of Southern California.
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