Shaping of microbial phenotypes by trade-offs.

Growth rate maximization is an important fitness strategy for microbes. However, the wide distribution of slow-growing oligotrophic microbes in ecosystems suggests that rapid growth is often not favored across ecological environments. In many circumstances, there exist trade-offs between growth and other important traits (e.g., adaptability and survival) due to physiological and proteome constraints. Investments on alternative traits could compromise growth rate and microbes need to adopt bet-hedging strategies to improve fitness in fluctuating environments. Here we review the mechanistic role of trade-offs in controlling bacterial growth and further highlight its ecological implications in driving the emergences of many important ecological phenomena such as co-existence, population heterogeneity and oligotrophic/copiotrophic lifestyles.

Integrated control of bacterial growth and stress response by (p)ppGpp in Escherichia coli: A seesaw fashion.

To thrive in nature, bacteria have to reproduce efficiently under favorable conditions and persist during stress. The global strategy that integrates the growth control and stress response remains to be explored. Here, we find that a moderate induction of (p)ppGpp reduces growth rate but significantly enhances the stress tolerance of E. coli, resulting from a global resource re-allocation from ribosome synthesis to the synthesis of stress-responsive proteins. Strikingly, the activation of stress response by (p)ppGpp is still largely retained in the absence of RpoS. In addition, (p)ppGpp induction could activate the catabolism of alanine and arginine, facilitating the adaption of bacteria to nutrient downshift. Our work demonstrates that the activation of stress response by (p)ppGpp could occur in an RpoS-independent manner and (p)ppGpp enables bacteria to integrate the control of growth and stress response in a seesaw fashion, thus acting as an important global regulator of the bacterial fitness landscape.

A fitness trade-off between growth and survival governed by Spo0A-mediated proteome allocation constraints in Bacillus subtilis.

Growth and survival are key determinants of bacterial fitness. However, how resource allocation of bacteria could reconcile these two traits to maximize fitness remains poorly understood. Here, we find that the resource allocation strategy of Bacillus subtilis does not lead to growth maximization on various carbon sources. Survival-related pathways impose strong proteome constraints on B. subtilis. Knockout of a master regulator gene, spo0A, triggers a global resource reallocation from survival-related pathways to biosynthesis pathways, further strongly stimulating the growth of B. subtilis. However, the fitness of spo0A-null strain is severely compromised because of various disadvantageous phenotypes (e.g., abolished sporulation and enhanced cell lysis). In particular, it also exhibits a strong defect in peptide utilization, being unable to efficiently recycle nutrients from the lysed cell debris to maintain long-term viability. Our work uncovers a fitness trade-off between growth and survival that governed by Spo0A-mediated proteome allocation constraints in B. subtilis, further shedding light on the fundamental design principle of bacteria.

Stringent response ensures the timely adaptation of bacterial growth to nutrient downshift.

Timely adaptation to nutrient downshift is crucial for bacteria to maintain fitness during feast and famine cycle in the natural niche. However, the molecular mechanism that ensures the timely adaption of bacterial growth to nutrient downshift remains poorly understood. Here, we quantitatively investigated the adaptation of Escherichia coli to various kinds of nutrient downshift. We found that relA deficient strain, which is devoid of stringent response, exhibits a significantly longer growth lag than wild type strain during adapting to both amino acid downshift and carbon downshift. Quantitative proteomics show that increased (p)ppGpp level promotes the growth adaption of bacteria to amino acid downshift via triggering the proteome resource re-allocation from ribosome synthesis to amino acid biosynthesis. Such type of proteome re-allocation is significantly delayed in the relA-deficient strain, which underlies its longer lag than wild type strain during amino acid downshift. During carbon downshift, a lack of stringent response in relA deficient strain leads to disruption of the transcription-translation coordination, thus compromising the transcription processivity and further the timely expression of related catabolic operons for utilizing secondary carbon sources. Our studies shed light on the fundamental strategy of bacteria to maintain fitness under nutrient-fluctuating environments.

Recent functional insights into the magic role of (p)ppGpp in growth control.

Rapid growth and survival are two key traits that enable bacterial cells to thrive in their natural habitat. The guanosine tetraphosphate and pentaphosphate [(p)ppGpp], also known as "magic spot", is a key second messenger inside bacterial cells as well as chloroplasts of plants and green algae. (p)ppGpp not only controls various stages of central dogma processes (replication, transcription, ribosome maturation and translation) and central metabolism but also regulates various physiological processes such as pathogenesis, persistence, motility and competence. Under extreme conditions such as nutrient starvation, (p)ppGpp-mediated stringent response is crucial for the survival of bacterial cells. This mini-review highlights some of the very recent progress on the key role of (p)ppGpp in bacterial growth control in light of cellular resource allocation and cell size regulation. We also briefly discuss some recent functional insights into the role of (p)ppGpp in plants and green algae from the angle of growth and development and further discuss several important open directions for future studies.

Quantitative analysis of asynchronous transcription-translation and transcription processivity in Bacillus subtilis under various growth conditions.

Tight coordination between transcription and translation has long been recognized as the hallmark of gene expression in bacteria. In Escherichia coli cells, disruption of the transcription-translation coordination leads to the loss of transcription processivity via triggering Rho-mediated premature transcription termination. Here we quantitatively characterize the transcription and translation kinetics in Gram-positive model bacterium Bacillus subtilis. We found that the speed of transcription elongation is much faster than that of translation elongation in B. subtilis under various growth conditions. Moreover, a Rho-independent loss of transcription processivity occurs constitutively in several genes/operons but is not subject to translational control. When the transcription elongation is decelerated under poor nutrients, low temperature, or nucleotide depletion, the loss of transcription processivity is strongly enhanced, suggesting that its degree is modulated by the speed of transcription elongation. Our study reveals distinct design principles of gene expression in E. coli and B. subtilis.

Control of ribosome synthesis in bacteria: the important role of rRNA chain elongation rate.

Bacteria growth depends crucially on protein synthesis, which is limited by ribosome synthesis. Ribosomal RNA (rRNA) transcription is the rate-limiting step of ribosome synthesis. It is generally proposed that the transcriptional initiation rate of rRNA operon is the primary factor that controls the rRNA synthesis. In this study, we established a convenient GFP-based reporter approach for measuring the bacterial rRNA chain elongation rate. We showed that the rRNA chain elongation rate of Escherichia coli remains constant under nutrient limitation and chloramphenicol inhibition. In contrast, rRNA chain elongation rate decreases dramatically under low temperatures. Strikingly, we found that Vibrio natriegens, the fastest growing bacteria known, has a 50% higher rRNA chain elongation rate than E. coli, which contributes to its rapid ribosome synthesis. Our study demonstrates that rRNA chain elongation rate is another important factor that affects the bacterial ribosome synthesis capacity.

Coupling of Ribosome Synthesis and Translational Capacity with Cell Growth.

Ribosome and protein synthesis lie at the core of cell growth and are major consumers of the cellular budget. Here we review recent progress in the coupling of ribosome synthesis and translational capacity with cell growth in bacteria. We elaborate on the different strategies of bacteria to modulate the protein synthesis rate at fast and slow growth rates. In particular, bacterial cells maintain translational potential at very slow growth as a strategy to keep fitness in fluctuating environments. We further discuss the important role of ribosome synthesis in rapidly proliferating eukaryotic cells such as yeast cells and cancer cells. The tight relation between ribosome and cell growth provides a broad research avenue for researchers from various disciplines.

Prevalence of overweight and obesity in China: Results from a cross-sectional study of 441 thousand adults, 2012-2015.

OBJECTIVES: Obesity has become a global health public problem. The study aims to examine the latest prevalence of overweight and obesity in China. METHODS: Data came from the China Hypertension Survey (CHS), a nationally representative cross-sectional study among residents aged ≥18 years from October 2012 to December 2015. Overweight and obesity were defined as 25≤BMI<30kg/m2 and BMI≥30kg/m2 according to the WHO classifications, respectively. RESULTS: The data of 441 306 participants were analyzed. The prevalence of overweight and obesity was 28.1% and 5.2% respectively. The prevalence of overweight and obesity varied considerably across provinces. The prevalence of overweight was the highest in Beijing, which was 2.8 fold of the lowest in Guangxi (40.9% vs. 14.6%). The prevalence of obesity was the highest in Tianjin, which was 9.4 fold of the lowest in Hainan (12.2% vs. 1.3%). There was a striking north-south gradient with the prevalence higher in Northeast and Northwest China and lower in Southeast China. Multivariate logistic regression analysis indicated that sex, age, education, smoking, marital status and family history of cardiovascular disease were significantly associated with overweight and obesity. CONCLUSIONS: Overweight and obesity are highly prevalent among Chinese adults, and their prevalence varies greatly among different population subgroups and provinces. National and provincial obesity control and prevention strategies should be public health priorities in China.

Bacterial stress defense: the crucial role of ribosome speed.

In nature, bacteria are constantly adapting to various stressful conditions. Timely activation of stress response programs is crucial for bacteria to smoothly survive under stressful conditions. Stress response, demanding the de novo synthesis of many defense proteins, is generally activated at the transcriptional level by specific regulators. However, the effect of the global protein translational status on stress response has been largely overlooked. The translational capacity is limited by the number of translating ribosomes and the translational elongation rate. Recent work has shown that certain environmental stressors (e.g. oxidative stress) could severely compromise the stress response progress of bacteria by causing either slow-down or even complete stalling of the translational elongation process. The maintenance of ribosome elongation rate, being crucial for timely synthesis of stress defense proteins, becomes the physiological bottleneck that limits the survival of bacteria in some stressful conditions. Here, we briefly summarize some recent progress on the translational status of bacteria under two distinct stress conditions, nutrient deprivation and oxidative stress. We further discuss several important open questions on the translational regulation of bacteria during stress. The ribosome translation should be investigated in parallel with traditional transcriptional regulation in order to gain a better understanding on bacterial stress defense.

Prevalence of Abdominal Obesity in China: Results from a Cross-Sectional Study of Nearly Half a Million Participants.

OBJECTIVE: This study aimed to examine the latest prevalence of abdominal obesity in China based on nationally representative data. METHODS: A stratified, multistage, random sampling method was used to obtain a nationally representative sample of residents aged ≥ 18 years from 31 provinces in mainland China from October 2012 to December 2015. Abdominal obesity was defined as a waist circumference ≥ 90 cm for men and a waist circumference ≥ 85 cm for women. RESULTS: The data of 441,306 participants were analyzed. The prevalence of abdominal obesity was 29.1% (28.6% in men and 29.6% in women); the number of adults with abdominal obesity was estimated to be 277.8 million (approximately 140.1 million in men and 137.7 million in women). The prevalence of abdominal obesity varied considerably among provinces. In general, the prevalence of abdominal obesity was higher in the northern, lower in the southern, higher in the western, and lower in the eastern areas of China. Besides the regional disparities, the prevalence of abdominal obesity varied greatly among different population subgroups. CONCLUSIONS: Abdominal obesity is highly prevalent among Chinese adults. National and provincial obesity control and prevention strategies should be public health priorities in China. To better control obesity, the underlying reasons for the regional disparities need to be addressed.

Disruption of transcription-translation coordination in Escherichia coli leads to premature transcriptional termination.

Tight coordination between transcription and translation is crucial to maintaining the integrity of gene expression in bacteria, yet how bacteria manage to coordinate these two processes remains unclear. Possible direct physical coupling between the RNA polymerase and ribosome has been thoroughly investigated in recent years. Here, we quantitatively characterize the transcriptional kinetics of Escherichia coli under different growth conditions. Transcriptional and translational elongation remain coordinated under various nutrient conditions, as previously reported. However, transcriptional elongation was not affected under antibiotics that slowed down translational elongation. This result was also found by introducing nonsense mutation that completely dissociated transcription from translation. Our data thus provide direct evidence that translation is not required to maintain the speed of transcriptional elongation. In cases where transcription and translation are dissociated, our study provides quantitative characterization of the resulting process of premature transcriptional termination (PTT). PTT-mediated polarity caused by translation-targeting antibiotics substantially affected the coordinated expression of genes in several long operons, contributing to the key physiological effects of these antibiotics. Our results also suggest a model in which the coordination between transcriptional and translational elongation under normal growth conditions is implemented by guanosine tetraphosphate.

Maintenance of translational elongation rate underlies the survival of Escherichia coli during oxidative stress.

To cope with harsh circumstances, bacterial cells must initiate cellular stress response programs, which demands the de novo synthesis of many stress defense proteins. Reactive oxygen species (ROS) is a universal environmental stressor for both prokaryotic cells and eukaryotic cells. However, the physiological burden that limits the survival of bacterial cells during oxidative stress remains elusive. Here we quantitatively characterize the cell growth and translational elongation rate of Escherichia coli cells treated with different doses of hydrogen peroxide. Cell growth is immediately arrested by low to moderate levels of hydrogen peroxide, but completely recovers after a certain lag time. The lag time depends positively on the dose of hydrogen peroxide. During the lag time, translational elongation rate drops by as much as ∼90% at initial stage and recovers to its normal state later, a phenomenon resulting from the dramatic alteration in cellular tRNA pools during oxidative stress. However, translational elongation is completely stalled at a certain threshold-level of hydrogen peroxide, at which cells ultimately fail to resume growth. Although the mRNA transcription of oxidative defense genes in oxyR regulon is dramatically induced upon hydrogen peroxide treatment, the extreme slow-down of translational elongation during high levels of hydrogen peroxide has severely compromised the timely synthesis of those oxidative defense proteins. Our study demonstrates that the tRNA-limited translational elongation is a key physiological bottleneck that the bacteria must overcome to counteract ROS, and the maintenance of translational elongation rate for timely synthesis of stress defense proteins is crucial for cells to smoothly get over the oxidative stress.

(p)ppGpp: the magic governor of bacterial growth economy.

A fundamental question in microbiology is how bacterial cells manage to coordinate gene expression with cell growth during adapting to various environmental conditions. Although the cellular responses to changing environments have been extensively studied using transcriptomic and proteomic approaches, it remains poorly understood regarding the molecular strategy enabling bacteria to manipulate the global gene expression patterns. The alarmone (p)ppGpp is a key secondary messenger involved in regulating various biochemical and physiological processes of bacterial cells. However, despite of the extensive studies of (p)ppGpp signaling in stringent response during the past 50 years, the connection between (p)ppGpp and exponential growth remains poorly understood. Our recent work demonstrates that (p)ppGpp is strongly involved in regulating cell growth of Escherichia coli through balancing the cellular investment on metabolic proteins and ribosomes, highlighting itself as a magic governor of bacterial global resource allocation. In this mini-review, we briefly summarize some historical perspectives and current progress of the relation between (p)ppGpp and bacterial exponential growth. Two important future directions are also highlighted: the first direction is to elucidate the cellular signal that triggers (p)ppGpp accumulation during poor growth conditions; the second direction is to investigate the relation between (p)ppGpp and exponential growth for bacterial species other than E. coli.

Growth suppression by altered (p)ppGpp levels results from non-optimal resource allocation in Escherichia coli.

Understanding how bacteria coordinate gene expression with biomass growth to adapt to various stress conditions remains a grand challenge in biology. Stress response is often associated with dramatic accumulation of cellular guanosine tetra- or penta-phosphate (p)ppGpp (also known as 'magic spot'), which is a key second messenger participating in regulating various biochemical and physiological processes of bacteria. Despite of the extensive studies on the mechanism of gene regulation by (p)ppGpp during stringent response, the connection between (p)ppGpp and bacterial steady-state exponential growth remains elusive. Here, we establish a versatile genetic approach to systematically perturb the (p)ppGpp level of Escherichia coli through titrating either the single-function (p)ppGpp synthetase or the singe-function (p)ppGpp hydrolase and quantitatively characterize cell growth and gene expression. Strikingly, increased and decreased (p)ppGpp levels both cause remarkable growth suppression of E. coli. From a coarse-grained insight, we demonstrate that increased (p)ppGpp levels limit ribosome synthesis while decreased (p)ppGpp levels limit the expression of metabolic proteins, both resulting in non-optimal resource allocation. Our study reveals a profound role of (p)ppGpp in regulating bacterial growth through governing global resource allocation. Moreover, we highlight the Mesh1 (p)ppGpp hydrolase from Drosophila melanogaster as a powerful genetic tool for interrogating bacterial (p)ppGpp physiology.

Sinorhizobium meliloti, a Slow-Growing Bacterium, Exhibits Growth Rate Dependence of Cell Size under Nutrient Limitation.

Bacterial cells need to coordinate the cell cycle with biomass growth to maintain cell size homeostasis. For fast-growing bacterial species like Escherichia coli and Bacillus subtilis, it is well-known that cell size exhibits a strong dependence on the growth rate under different nutrient conditions (known as the nutrient growth law). However, cell size changes little with slow growth (doubling time of >90 min) for E. coli, posing the interesting question of whether slow-growing bacteria species also observe the nutrient growth law. Here, we quantitatively characterize the cell size and cell cycle parameter of a slow-growing bacterium, Sinorhizobium meliloti, at different nutrient conditions. We find that S. meliloti exhibits a threefold change in its cell size when its doubling time varies from 2 h to 6 h. Moreover, the progression rate of its cell cycle is much longer than that of E. coli, suggesting a delicate coordination between the cell cycle progression rate and the biomass growth rate. Our study shows that the nutrient growth law holds robustly regardless of the growth capacity of the bacterial species, generalizing its applicability among the bacterial kingdom.IMPORTANCE The dependence of cell size on growth rate is a fundamental principle in the field of bacterial cell size regulation. Previous studies of cell size regulation mainly focus on fast-growing bacterial species such as Escherichia coli and Bacillussubtilis We find here that Sinorhizobium meliloti, a slow-growing bacterium, exhibits a remarkable growth rate-dependent cell size pattern under nutrient limitation, generalizing the applicability of the empirical nutrient growth law of cell size. Moreover, S. meliloti exhibits a much slower speed of cell cycle progression than E. coli does, suggesting a delicate coordination between the cell cycle progression rate and the biomass growth rate.

High Osmolarity Modulates Bacterial Cell Size through Reducing Initiation Volume in Escherichia coli.

Bacterial cell size is closely associated with biomass growth and cell cycle progression, including chromosome replication and cell division. It is generally proposed that Escherichia coli cells tightly control the timing of chromosome replication through maintaining a constant cell volume per origin upon initiating chromosome replication (constant initiation volume) under various growth conditions. Here, we quantitatively characterize the cell size and cell cycle of Escherichia coli cells growing exponentially under hyperosmotic stress, which is a common environmental stressor that profoundly affects the bacterial water content. The bacterial cell size is reduced by hyperosmotic stress, even though the C and D periods are remarkably prolonged, indicating a significantly reduced initiation volume. The reduced initiation volume originates from the higher concentration of DnaA initiator protein caused by water loss at high osmolarity. Our study shows suggests a fundamental role of water content in regulating bacterial cell size and has also revealed a new role of the DnaA protein in regulating the chromosome replication elongation beyond regulating the replication initiation process.IMPORTANCE Bacterial cell size depends on growth rate, cell cycle progression, and the cell volume per origin upon initiating chromosome replication (initiation volume). Here, we perform the first systematic and quantitative study of the effect of hyperosmotic stress on the E. coli cell size and cell cycle. We find that hyperosmotic stress significantly reduces the initiation volume. The reduced initiation volume is attributed to the increased DnaA concentration caused by water loss at high osmolarity, indicating a fundamental role of water content in cell size and cell cycle regulation.

Central Aortic Systolic Blood Pressure Exhibits Advantages Over Brachial Blood Pressure Measurements in Chronic Kidney Disease Risk Prediction in Women.

BACKGROUND/AIMS: To investigate whether the invasively obtained central aortic systolic blood pressure (CSBP) predicts chronic kidney disease (CKD) better than brachial systolic blood pressure (SBP), brachial diastolic blood pressure (DBP) and brachial pulse pressure (PP) in the middle-aged Chinese population. METHODS: A cross-sectional study was carried out across China in 2009-2010 among the subjects aged 35-64 years. CSBP was measured non-invasively by radial artery applanation tonometry B-pro (A-PULSE CASP and corresponding software). CSBP, SBP, DBP and PP were standardized with Z-score and the odds ratios were calculated with multivariable logistic regression model. RESULTS: Data of 10197 participants were analyzed. The multivariable logistic regression after adjusting for possible confounders showed that a 1-standard deviation increment in each blood pressure measurement was associated with greater risk of CKD in both men and women (P < 0.05). The association of CSBP with CKD was stronger than SBP, DBP and PP in women, while in men the association of CSBP with CKD was stronger only than PP. With CSBP and SBP entering into the multivariable logistic regression models jointly, the odds ratio (95% confidence interval) for CSBP and SBP was 1.57 (1.39-1.79) and 1.22 (1.07-1.38) in women and 1.20 (1.03-1.39) and 1.48 (1.28-1.72) in men, respectively. With CSBP and DBP entering into the multivariable logistic regression models jointly, the odds ratio (95% confidence interval) for CSBP and DBP was 1.68 (1.52-1.84) and 1.15 (1.04-1.27) in women and 1.30 (1.15-1.46) and 1.45 (1.29-1.63) in men, respectively. With CSBP and PP entering into the multivariable logistic regression models jointly, the odds ratio (95% confidence interval) for CSBP and PP was 1.75 (1.58-1.94) and 1.06 (0.96-1.17) in women and 1.58 (1.41-1.77) and 1.04 (0.93-1.17) in men, respectively. CONCLUSION: CSBP and brachial blood pressure measurements are all predictors of CKD, however the non-invasively obtained CSBP may offer advantages over brachial blood pressure measurements in CKD risk prediction in women.