1
|
Liu Y, LaBonte S, Brake C, LaFayette C, Rosebrock AP, Caudy AA, Straight PD. MOB rules: Antibiotic Exposure Reprograms Metabolism to Mobilize Bacillus subtilis in Competitive Interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585991. [PMID: 38562742 PMCID: PMC10983992 DOI: 10.1101/2024.03.20.585991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Antibiotics have dose-dependent effects on exposed bacteria. The medicinal use of antibiotics relies on their growth-inhibitory activities at sufficient concentrations. At subinhibitory concentrations, exposure effects vary widely among different antibiotics and bacteria. Bacillus subtilis responds to bacteriostatic translation inhibitors by mobilizing a population of cells (MOB-Mobilized Bacillus) to spread across a surface. How B. subtilis regulates the antibiotic-induced mobilization is not known. In this study, we used chloramphenicol to identify regulatory functions that B. subtilis requires to coordinate cell mobilization following subinhibitory exposure. We measured changes in gene expression and metabolism and mapped the results to a network of regulatory proteins that direct the mobile response. Our data reveal that several transcriptional regulators coordinately control the reprogramming of metabolism to support mobilization. The network regulates changes in glycolysis, nucleotide metabolism, and amino acid metabolism that are signature features of the mobilized population. Among the hundreds of genes with changing expression, we identified two, pdhA and pucA, where the magnitudes of their changes in expression, and in the abundance of associated metabolites, reveal hallmark metabolic features of the mobilized population. Using reporters of pdhA and pucA expression, we visualized the separation of major branches of metabolism in different regions of the mobilized population. Our results reveal a regulated response to chloramphenicol exposure that enables a population of bacteria in different metabolic states to mount a coordinated mobile response.
Collapse
Affiliation(s)
- Yongjin Liu
- Biochemistry and Biophysics Department, Texas A&M University, AgriLife Research, College Station, Texas, USA
| | - Sandra LaBonte
- Biochemistry and Biophysics Department, Texas A&M University, AgriLife Research, College Station, Texas, USA
- Interdisciplinary Program in Genetics and Genomics,Texas A&M University, College Station, Texas, USA
| | - Courtney Brake
- Department of Visualization, Institute for Applied Creativity, Texas A&M University, College Station, Texas, USA
| | - Carol LaFayette
- Department of Visualization, Institute for Applied Creativity, Texas A&M University, College Station, Texas, USA
| | | | - Amy A. Caudy
- Maple Flavored Solutions, LLC, Indianapolis, Indiana, USA
| | - Paul D. Straight
- Biochemistry and Biophysics Department, Texas A&M University, AgriLife Research, College Station, Texas, USA
- Interdisciplinary Program in Genetics and Genomics,Texas A&M University, College Station, Texas, USA
| |
Collapse
|
2
|
Ciolli Mattioli C, Eisner K, Rosenbaum A, Wang M, Rivalta A, Amir A, Golding I, Avraham R. Physiological stress drives the emergence of a Salmonella subpopulation through ribosomal RNA regulation. Curr Biol 2023; 33:4880-4892.e14. [PMID: 37879333 PMCID: PMC10843543 DOI: 10.1016/j.cub.2023.09.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/24/2023] [Accepted: 09/26/2023] [Indexed: 10/27/2023]
Abstract
Bacteria undergo cycles of growth and starvation to which they must adapt swiftly. One important strategy for adjusting growth rates relies on ribosomal levels. Although high ribosomal levels are required for fast growth, their dynamics during starvation remain unclear. Here, we analyzed ribosomal RNA (rRNA) content of individual Salmonella cells by using fluorescence in situ hybridization (rRNA-FISH) and measured a dramatic decrease in rRNA numbers only in a subpopulation during nutrient limitation, resulting in a bimodal distribution of cells with high and low rRNA content. During nutritional upshifts, the two subpopulations were associated with distinct phenotypes. Using a transposon screen coupled with rRNA-FISH, we identified two mutants, DksA and RNase I, acting on rRNA transcription shutdown and degradation, which abolished the formation of the subpopulation with low rRNA content. Our work identifies a bacterial mechanism for regulation of ribosomal bimodality that may be beneficial for population survival during starvation.
Collapse
Affiliation(s)
- Camilla Ciolli Mattioli
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Kfir Eisner
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Aviel Rosenbaum
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Mengyu Wang
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andre' Rivalta
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ariel Amir
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ido Golding
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Roi Avraham
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
| |
Collapse
|
3
|
Takano S, Takahashi H, Yama Y, Miyazaki R, Furusawa C, Tsuru S. Inference of transcriptome signatures of Escherichia coli in long-term stationary phase. Sci Rep 2023; 13:5647. [PMID: 37024648 PMCID: PMC10079935 DOI: 10.1038/s41598-023-32525-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 03/29/2023] [Indexed: 04/08/2023] Open
Abstract
"Non-growing" is a dominant life form of microorganisms in nature, where available nutrients and resources are limited. In laboratory culture systems, Escherichia coli can survive for years under starvation, denoted as long-term stationary phase, where a small fraction of cells manages to survive by recycling resources released from nonviable cells. Although the physiology by which viable cells in long-term stationary phase adapt to prolonged starvation is of great interest, their genome-wide response has not been fully understood. In this study, we analyzed transcriptional profiles of cells exposed to the supernatant of 30-day long-term stationary phase culture and found that their transcriptome profiles displayed several similar responses to those of cells in the 16-h short-term stationary phase. Nevertheless, our results revealed that cells in long-term stationary phase supernatant exhibit higher expressions of stress-response genes such as phage shock proteins (psp), and lower expressions of growth-related genes such as ribosomal proteins than those in the short-term stationary phase. We confirmed that the mutant lacking the psp operon showed lower survival and growth rate in the long-term stationary phase culture. This study identified transcriptional responses for stress-resistant physiology in the long-term stationary phase environment.
Collapse
Affiliation(s)
- Sotaro Takano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- International Center for Materials Nanoarchitectonics (NIMS), Research Center for Macromolecules and Biomaterials, Tsukuba, Japan
| | - Hiromi Takahashi
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Yoshie Yama
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Ryo Miyazaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Computational Bio Big Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo, Japan
| | - Chikara Furusawa
- Graduate School of Science, Universal Biology Institute, The University of Tokyo, Tokyo, Japan
- Center for Biosystem Dynamics Research, RIKEN, Kobe, Japan
| | - Saburo Tsuru
- Graduate School of Science, Universal Biology Institute, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
4
|
Distinct Survival, Growth Lag, and rRNA Degradation Kinetics during Long-Term Starvation for Carbon or Phosphate. mSphere 2022; 7:e0100621. [PMID: 35440180 PMCID: PMC9241543 DOI: 10.1128/msphere.01006-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The stationary phase is the general term for the state a bacterial culture reaches when no further increase in cell mass occurs due to exhaustion of nutrients in the growth medium. Depending on the type of nutrient that is first depleted, the metabolic state of the stationary phase cells may vary greatly, and the subsistence strategies that best support cell survival may differ. As ribosomes play a central role in bacterial growth and energy expenditure, ribosome preservation is a key element of such strategies. To investigate the degree of ribosome preservation during long-term starvation, we compared the dynamics of rRNA levels of carbon-starved and phosphorus-starved Escherichia coli cultures for up to 28 days. The starved cultures' contents of full-length 16S and 23S rRNA decreased as the starvation proceeded in both cases, and phosphorus starvation resulted in much more rapid rRNA degradation than carbon starvation. Bacterial survival and regrowth kinetics were also quantified. Upon replenishment of the nutrient in question, carbon-starved cells resumed growth faster than cells starved for phosphate for the equivalent amount of time, and for both conditions, the lag time increased with the starvation time. While these results are in accordance with the hypothesis that cells with a larger ribosome pool recover more readily upon replenishment of nutrients, we also observed that the lag time kept increasing with increasing starvation time, also when the amount of rRNA per viable cell remained constant, highlighting that lag time is not a simple function of ribosome content under long-term starvation conditions. IMPORTANCE The exponential growth of bacterial populations is punctuated by long or short periods of starvation lasting from the point of nutrient exhaustion until nutrients are replenished. To understand the consequences of long-term starvation for Escherichia coli cells, we performed month-long carbon and phosphorus starvation experiments and measured three key phenotypes of the cultures, namely, the survival of the cells, the time needed for them to resume growth after nutrient replenishment, and the levels of intact rRNA preserved in the cultures. The starved cultures' concentration of rRNA dropped with starvation time, as did cell survival, while the lag time needed for regrowth increased. While all three phenotypes were more severely affected during starvation for phosphorus than for carbon, our results demonstrate that neither survival nor lag time is correlated with ribosome content in a straightforward manner.
Collapse
|
5
|
Mohiuddin SG, Ghosh S, Ngo HG, Sensenbach S, Karki P, Dewangan NK, Angardi V, Orman MA. Cellular Self-Digestion and Persistence in Bacteria. Microorganisms 2021; 9:2269. [PMID: 34835393 PMCID: PMC8626048 DOI: 10.3390/microorganisms9112269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/30/2022] Open
Abstract
Cellular self-digestion is an evolutionarily conserved process occurring in prokaryotic cells that enables survival under stressful conditions by recycling essential energy molecules. Self-digestion, which is triggered by extracellular stress conditions, such as nutrient depletion and overpopulation, induces degradation of intracellular components. This self-inflicted damage renders the bacterium less fit to produce building blocks and resume growth upon exposure to fresh nutrients. However, self-digestion may also provide temporary protection from antibiotics until the self-digestion-mediated damage is repaired. In fact, many persistence mechanisms identified to date may be directly or indirectly related to self-digestion, as these processes are also mediated by many degradative enzymes, including proteases and ribonucleases (RNases). In this review article, we will discuss the potential roles of self-digestion in bacterial persistence.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Mehmet A. Orman
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77004, USA; (S.G.M.); (S.G.); (H.G.N.); (S.S.); (P.K.); (N.K.D.); (V.A.)
| |
Collapse
|
6
|
Li Y, Sharma MR, Koripella RK, Banavali NK, Agrawal RK, Ojha AK. Ribosome hibernation: a new molecular framework for targeting nonreplicating persisters of mycobacteria. MICROBIOLOGY-SGM 2021; 167. [PMID: 33555244 DOI: 10.1099/mic.0.001035] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Treatment of tuberculosis requires a multi-drug regimen administered for at least 6 months. The long-term chemotherapy is attributed in part to a minor subpopulation of nonreplicating Mycobacterium tuberculosis cells that exhibit phenotypic tolerance to antibiotics. The origins of these cells in infected hosts remain unclear. Here we discuss some recent evidence supporting the hypothesis that hibernation of ribosomes in M. tuberculosis, induced by zinc starvation, could be one of the primary mechanisms driving the development of nonreplicating persisters in hosts. We further analyse inconsistencies in previously reported studies to clarify the molecular principles underlying mycobacterial ribosome hibernation.
Collapse
Affiliation(s)
- Yunlong Li
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Manjuli R Sharma
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Ravi K Koripella
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Nilesh K Banavali
- Department of Biomedical Sciences, University at Albany, Albany, NY, USA.,Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Rajendra K Agrawal
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA.,Department of Biomedical Sciences, University at Albany, Albany, NY, USA
| | - Anil K Ojha
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA.,Department of Biomedical Sciences, University at Albany, Albany, NY, USA
| |
Collapse
|
7
|
Gummesson B, Shah SA, Borum AS, Fessler M, Mitarai N, Sørensen MA, Svenningsen SL. Valine-Induced Isoleucine Starvation in Escherichia coli K-12 Studied by Spike-In Normalized RNA Sequencing. Front Genet 2020; 11:144. [PMID: 32211022 PMCID: PMC7066862 DOI: 10.3389/fgene.2020.00144] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/07/2020] [Indexed: 12/19/2022] Open
Abstract
Escherichia coli cells respond to a period of famine by globally reorganizing their gene expression. The changes are known as the stringent response, which is orchestrated by the alarmone ppGpp that binds directly to RNA polymerase. The resulting changes in gene expression are particularly well studied in the case of amino acid starvation. We used deep RNA sequencing in combination with spike-in cells to measure global changes in the transcriptome after valine-induced isoleucine starvation of a standard E. coli K12 strain. Owing to the whole-cell spike-in method that eliminates variations in RNA extraction efficiency between samples, we show that ribosomal RNA levels are reduced during isoleucine starvation and we quantify how the change in cellular RNA content affects estimates of gene regulation. Specifically, we show that standard data normalization relying on sample sequencing depth underestimates the number of down-regulated genes in the stringent response and overestimates the number of up-regulated genes by approximately 40%. The whole-cell spike-in method also made it possible to quantify how rapidly the pool of total messenger RNA (mRNA) decreases upon amino acid starvation. A principal component analysis showed that the first two components together described 69% of the variability of the data, underlining that large and highly coordinated regulons are at play in the stringent response. The induction of starvation by sudden addition of high valine concentrations provoked prominent regulatory responses outside of the expected ppGpp, RpoS, and Lrp regulons. This underlines the notion that with the high resolution possible in deep RNA sequencing analysis, any different starvation method (e.g., nitrogen-deprivation, removal of an amino acid from an auxotroph strain, or valine addition to E. coli K12 strains) will produce measurable variations in the stress response produced by the cells to cope with the specific treatment.
Collapse
Affiliation(s)
- Bertil Gummesson
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Shiraz Ali Shah
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Mathias Fessler
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Namiko Mitarai
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | |
Collapse
|
8
|
Trösch R, Willmund F. The conserved theme of ribosome hibernation: from bacteria to chloroplasts of plants. Biol Chem 2020; 400:879-893. [PMID: 30653464 DOI: 10.1515/hsz-2018-0436] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/03/2019] [Indexed: 12/21/2022]
Abstract
Cells are highly adaptive systems that respond and adapt to changing environmental conditions such as temperature fluctuations or altered nutrient availability. Such acclimation processes involve reprogramming of the cellular gene expression profile, tuning of protein synthesis, remodeling of metabolic pathways and morphological changes of the cell shape. Nutrient starvation can lead to limited energy supply and consequently, remodeling of protein synthesis is one of the key steps of regulation since the translation of the genetic code into functional polypeptides may consume up to 40% of a cell's energy during proliferation. In eukaryotic cells, downregulation of protein synthesis during stress is mainly mediated by modification of the translation initiation factors. Prokaryotic cells suppress protein synthesis by the active formation of dimeric so-called 'hibernating' 100S ribosome complexes. Such a transition involves a number of proteins which are found in various forms in prokaryotes but also in chloroplasts of plants. Here, we review the current understanding of these hibernation factors and elaborate conserved principles which are shared between species.
Collapse
Affiliation(s)
- Raphael Trösch
- Department of Biology, Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Straße 23, D-67663 Kaiserslautern, Germany
| | - Felix Willmund
- Department of Biology, Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Straße 23, D-67663 Kaiserslautern, Germany
| |
Collapse
|
9
|
Fessler M, Gummesson B, Charbon G, Svenningsen SL, Sørensen MA. Short‐term kinetics of rRNA degradation inEscherichia coliupon starvation for carbon, amino acid or phosphate. Mol Microbiol 2020; 113:951-963. [DOI: 10.1111/mmi.14462] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 11/27/2022]
Affiliation(s)
- Mathias Fessler
- Department of Biology University of Copenhagen Copenhagen N Denmark
- DTU Environment Technical University of Denmark Kongens Lyngby Denmark
| | - Bertil Gummesson
- Department of Biology University of Copenhagen Copenhagen N Denmark
| | | | | | | |
Collapse
|
10
|
Sørensen MA, Fehler AO, Lo Svenningsen S. Transfer RNA instability as a stress response in Escherichia coli: Rapid dynamics of the tRNA pool as a function of demand. RNA Biol 2018; 15:586-593. [PMID: 29023189 PMCID: PMC6103710 DOI: 10.1080/15476286.2017.1391440] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Production of the translation apparatus of E. coli is carefully matched to the demand for protein synthesis posed by a given growth condition. For example, the fraction of RNA polymerases that transcribe rRNA and tRNA drops from 80% during rapid growth to 24% within minutes of a sudden amino acid starvation. We recently reported in Nucleic Acids Research that the tRNA pool is more dynamically regulated than previously thought. In addition to the regulation at the level of synthesis, we found that tRNAs are subject to demand-based regulation at the level of their degradation. In this point-of-view article we address the question of why this phenomenon has not previously been described. We also present data that expands on the mechanism of tRNA degradation, and we discuss the possible implications of tRNA instability for the ability of E. coli to cope with stresses that affect the translation process.
Collapse
|
11
|
Stenum TS, Sørensen MA, Svenningsen SL. Quantification of the Abundance and Charging Levels of Transfer RNAs in Escherichia coli. J Vis Exp 2017. [PMID: 28872118 DOI: 10.3791/56212] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Transfer RNA (tRNA) is an essential part of the translational machinery in any organism. tRNAs bind and transfer amino acids to the translating ribosome. The relative levels of different tRNAs, and the ratio of aminoacylated tRNA to total tRNA, known as the charging level, are important factors in determining the accuracy and speed of translation. Therefore, the abundance and charging levels of tRNAs are important variables to measure when studying protein synthesis, for example under various stress conditions. Here, we describe a method for harvesting tRNA and directly measuring both the relative abundance and the absolute charging level of specific tRNA species in Escherichia coli. The tRNA is harvested in such a way that the labile bond between the tRNA and its amino acid is preserved. The RNA is then subjected to gel electrophoresis and Northern blotting, which results in separation of the charged and uncharged tRNAs. The levels of specific tRNAs in different samples can be compared due to the addition of spike-in cells for normalization. Prior to RNA purification, we add 5% of E. coli cells that overproduce the rare tRNAselC to each sample. The amount of the tRNA species of interest in a sample is then normalized to the amount of tRNAselC in the same sample. Addition of spike-in cells prior to RNA purification has the advantage over addition of purified spike-in RNAs that it also accounts for any differences in cell lysis efficiency between samples.
Collapse
|
12
|
Density-Dependent Recycling Promotes the Long-Term Survival of Bacterial Populations during Periods of Starvation. mBio 2017; 8:mBio.02336-16. [PMID: 28174316 PMCID: PMC5296608 DOI: 10.1128/mbio.02336-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The amount of natural resources in the Earth’s environment is in flux, which can trigger catastrophic collapses of ecosystems. How populations survive under nutrient-poor conditions is a central question in ecology. Curiously, some bacteria persist for a long time in nutrient-poor environments. Although this survival may be accomplished through cell death and the recycling of dead cells, the importance of these processes and the mechanisms underlying the survival of the populations have not been quantitated. Here, we use microbial laboratory experiments and mathematical models to demonstrate that death and recycling are essential activities for the maintenance of cell survival. We also show that the behavior of the survivors is governed by population density feedback, wherein growth is limited not only by the available resources but also by the population density. The numerical simulations suggest that population density-dependent recycling could be an advantageous behavior under starvation conditions. How organisms survive after exhaustion of resources is a central question in ecology. Starving Escherichia coli constitute a model system to understand survival mechanisms during long-term starvation. Although death and the recycling of dead cells might play a key role in the maintenance of long-term survival, their mechanisms and importance have not been quantitated. Here, we verified the significance of social recycling of dead cells for long-term survival. We also show that the survivors restrained their recycling and did not use all available nutrients released from dead cells, which may be advantageous under starvation conditions. These results indicate that not only the utilization of dead cells but also restrained recycling coordinate the effective utilization of limited resources for long-term survival under starvation.
Collapse
|
13
|
Svenningsen SL, Kongstad M, Stenum TS, Muñoz-Gómez AJ, Sørensen MA. Transfer RNA is highly unstable during early amino acid starvation in Escherichia coli. Nucleic Acids Res 2017; 45:793-804. [PMID: 27903898 PMCID: PMC5314770 DOI: 10.1093/nar/gkw1169] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 11/02/2016] [Accepted: 11/09/2016] [Indexed: 11/17/2022] Open
Abstract
Due to its long half-life compared to messenger RNA, bacterial transfer RNA is known as stable RNA. Here, we show that tRNAs become highly unstable as part of Escherichia coli's response to amino acid starvation. Degradation of the majority of cellular tRNA occurs within twenty minutes of the onset of starvation for each of several amino acids. Both the non-cognate and cognate tRNA for the amino acid that the cell is starving for are degraded, and both charged and uncharged tRNA species are affected. The alarmone ppGpp orchestrates the stringent response to amino acid starvation. However, tRNA degradation occurs in a ppGpp-independent manner, as it occurs with similar kinetics in a relaxed mutant. Further, we also observe rapid tRNA degradation in response to rifampicin treatment, which does not induce the stringent response. We propose a unifying model for these observations, in which the surplus tRNA is degraded whenever the demand for protein synthesis is reduced. Thus, the tRNA pool is a highly regulated, dynamic entity. We propose that degradation of surplus tRNA could function to reduce mistranslation in the stressed cell, because it would reduce competition between cognate and near-cognate charged tRNAs at the ribosomal A-site.
Collapse
Affiliation(s)
| | - Mette Kongstad
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | | | - Ana J Muñoz-Gómez
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Michael A Sørensen
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| |
Collapse
|
14
|
Hu LZ, Zhang WP, Zhou MT, Han QQ, Gao XL, Zeng HL, Guo L. Analysis of Salmonella PhoP/PhoQ regulation by dimethyl-SRM-based quantitative proteomics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:20-8. [PMID: 26472331 DOI: 10.1016/j.bbapap.2015.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/29/2015] [Accepted: 10/09/2015] [Indexed: 02/01/2023]
Abstract
SRM (selected reaction monitoring), a tandem mass spectrometry-based method characterized by high repeatability and accuracy, is an effective tool for the quantification of predetermined proteins. In this study, we built a time-scheduled dimethyl-SRM method that can provide the precise relative quantification of 92 proteins in one run. By applying this method to the Salmonella PhoP/PhoQ two-component system, we found that the expression of selected PhoP/PhoQ-activated proteins in response to Mg(2+) concentrations could be divided into two distinct patterns. For the time-course SRM experiment, we found that the dynamics of the selected PhoP/PhoQ-activated proteins could be divided into three distinct patterns, providing a new clue regarding PhoP/PhoQ activation and regulation. Moreover, the results for iron homeostasis proteins in response to Mg(2+) concentrations revealed that the PhoP/PhoQ two-component system may serve as a repressor for iron uptake proteins. And ribosomal protein levels clearly showed a response to different Mg(2+) concentrations and to time.
Collapse
Affiliation(s)
- Li-Zhi Hu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wei-Ping Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mao-Tian Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qiang-Qiang Han
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiao-Li Gao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hao-Long Zeng
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lin Guo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China.
| |
Collapse
|
15
|
Mahalik S, Sharma AK, Mukherjee KJ. Genome engineering for improved recombinant protein expression in Escherichia coli. Microb Cell Fact 2014; 13:177. [PMID: 25523647 PMCID: PMC4300154 DOI: 10.1186/s12934-014-0177-1] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/05/2014] [Indexed: 01/09/2023] Open
Abstract
A metabolic engineering perspective which views recombinant protein
expression as a multistep pathway allows us to move beyond vector design and
identify the downstream rate limiting steps in expression. In E.coli these are typically at the translational level
and the supply of precursors in the form of energy, amino acids and nucleotides.
Further recombinant protein production triggers a global cellular stress response
which feedback inhibits both growth and product formation. Countering this requires
a system level analysis followed by a rational host cell engineering to sustain
expression for longer time periods. Another strategy to increase protein yields
could be to divert the metabolic flux away from biomass formation and towards
recombinant protein production. This would require a growth stoppage mechanism which
does not affect the metabolic activity of the cell or the transcriptional or
translational efficiencies. Finally cells have to be designed for efficient export
to prevent buildup of proteins inside the cytoplasm and also simplify downstream
processing. The rational and the high throughput strategies that can be used for the
construction of such improved host cell platforms for recombinant protein expression
is the focus of this review.
Collapse
Affiliation(s)
- Shubhashree Mahalik
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Ashish K Sharma
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Krishna J Mukherjee
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
| |
Collapse
|
16
|
Nai YH, Zemb O, Gutierrez-Zamora ML, Manefield M, Powell SM, Breadmore MC. Capillary electrophoresis ribosomal RNA single-stranded conformation polymorphism: a new approach for characterization of low-diversity microbial communities. Anal Bioanal Chem 2012; 404:1897-906. [PMID: 22865007 DOI: 10.1007/s00216-012-6268-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 07/11/2012] [Accepted: 07/12/2012] [Indexed: 11/28/2022]
Abstract
Capillary electrophoresis (CE) has been the principle system for nucleic acid analysis since the early 1990s due to its inherent advantages such as fast analysis time, high resolution and efficiency, minimal sample requirement, high detection sensitivity, and automation. In the past few decades, microbial community fingerprinting methods such as terminal restriction fragment length polymorphism and single-stranded conformation polymorphism (SSCP) have migrated to CE to utilize its advantages over conventional slab gel electrophoresis. Recently, a gel-based direct rRNA fingerprint method was demonstrated. Different from other existing microbial community characterization approaches, this novel approach is polymerase chain reaction free and capable of providing information on the relative abundance of rRNA from individual phylotypes in low-diversity samples. As a gel-based method, it has a long analysis time and relatively large reagent and sample requirements. Here, we addressed these limitations by transferring the RNA fingerprint approach to the CE platform. Analysis time significantly improved from 24 h to 60 min, and the use of a fluorescently labeled hybridization probe as the detection strategy decreased the sample requirement by ten-fold. The combination of fast analysis time, low sample requirement, and sensitive fluorescence detection makes CE-RNA-SSCP an appealing new approach for characterizing low-diversity microbial communities.
Collapse
Affiliation(s)
- Yi H Nai
- Australian Centre for Research on Separation Science (ACROSS), School of Chemistry, University of Tasmania, Hobart, TAS, Australia
| | | | | | | | | | | |
Collapse
|
17
|
Ribosome degradation in growing bacteria. EMBO Rep 2011; 12:458-62. [PMID: 21460796 PMCID: PMC3090016 DOI: 10.1038/embor.2011.47] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 01/21/2011] [Accepted: 03/03/2011] [Indexed: 11/09/2022] Open
Abstract
Ribosomes are large ribozymes that synthesize all cellular proteins. As protein synthesis is rate-limiting for bacterial growth and ribosomes can comprise a large portion of the cellular mass, elucidation of ribosomal turnover is important to the understanding of cellular physiology. Although ribosomes are widely believed to be stable in growing cells, this has never been rigorously tested, owing to the lack of a suitable experimental system in commonly used bacterial model organisms. Here, we develop an experimental system to directly measure ribosomal stability in Escherichia coli. We show that (i) ribosomes are stable when cells are grown at a constant rate in the exponential phase; (ii) more than half of the ribosomes made during exponential growth are degraded during slowing of culture growth preceding the entry into stationary phase; and (iii) ribosomes are stable for many hours in the stationary phase. Ribosome degradation occurs in growing cultures that contain almost no dead cells and coincides with a reduction of comparable magnitude in the cellular RNA concentration.
Collapse
|
18
|
A role for a bacterial ortholog of the Ro autoantigen in starvation-induced rRNA degradation. Proc Natl Acad Sci U S A 2010; 107:4022-7. [PMID: 20160119 DOI: 10.1073/pnas.1000307107] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cellular adaptations to stress often involve changes in RNA metabolism. One RNA-binding protein that has been implicated in RNA handling during environmental stress in both animal cells and prokaryotes is the Ro autoantigen. However, the function of Ro in stress conditions has been unknown. We report that a Ro protein in the radiation-resistant eubacterium Deinococcus radiodurans participates in ribosomal RNA (rRNA) degradation during growth in stationary phase, a form of starvation. Levels of the Ro ortholog Rsr increase dramatically during growth in stationary phase and the presence of Rsr confers a growth advantage. Examination of rRNA profiles reveals that Rsr, the 3' to 5' exoribonuclease polynucleotide phosphorylase (PNP) and additional nucleases are all involved in the extensive rRNA decay that occurs during starvation of this bacterium. We show that Rsr, PNP, and an Rsr-PNP complex exhibit increased sedimentation with ribosomal subunits during stationary phase. As the fractionation of PNP with ribosomal subunits is strongly enhanced in the presence of Rsr, we propose that Ro proteins function as cofactors to increase the association of exonucleases with certain substrates during stress.
Collapse
|
19
|
Kölsch G, Matz-Grund C, Pedersen BV. Ultrastructural and molecular characterization of endosymbionts of the reed beetle genusMacroplea(Chrysomelidae, Donaciinae), and proposal of “CandidatusMacropleicola appendiculatae” and “CandidatusMacropleicola muticae”. Can J Microbiol 2009; 55:1250-60. [DOI: 10.1139/w09-085] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Intracellular bacterial symbionts are known from various insect groups, particularly from those feeding on unbalanced diets, where the bacteria provide essential nutrients to the host. In the case of reed beetles (Coleoptera: Chrysomelidae, Donaciinae), however, the endosymbionts appear to be associated with specialized “glands” that secrete a material used for the beetles’ unusual water-tight cocoon. These glands were discovered over a century ago, but the bacteria they contain have yet to be characterized and placed in a phylogenetic context. Here, we describe the ultrastructure of two endosymbiotic species (“ Candidatus Macropleicola appendiculatae” and “ Candidatus Macropleicola muticae”) that reside in cells of the Malpighian tubules of the reed beetle species Macroplea appendiculata and Macroplea mutica , respectively. Fluorescent in situ hybridization using oligonucleotides targeting the 16S rRNA gene specific to Macroplea symbionts verified the localization of the symbionts in these organs. Phylogenetic analysis of 16S rRNA placed “Candidatus Macropleicola” in a clade of typically endosymbiotic Enterobacteriaceae (γ-proteobacteria). Finally, we discuss the evidence available for the hypothesis that the beetle larvae use a secretion produced by the bacteria for the formation of an underwater cocoon.
Collapse
Affiliation(s)
- Gregor Kölsch
- Zoological Institute, Department of Molecular Evolutionary Biology, University of Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany
- Zoological Institute, Animal Ecology, University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
- University of Copenhagen, Department of Biology, Universitetsparken 15, DK 2100 Copenhagen Ø, Denmark
| | - Corinna Matz-Grund
- Zoological Institute, Department of Molecular Evolutionary Biology, University of Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany
- Zoological Institute, Animal Ecology, University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
- University of Copenhagen, Department of Biology, Universitetsparken 15, DK 2100 Copenhagen Ø, Denmark
| | - Bo V. Pedersen
- Zoological Institute, Department of Molecular Evolutionary Biology, University of Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany
- Zoological Institute, Animal Ecology, University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
- University of Copenhagen, Department of Biology, Universitetsparken 15, DK 2100 Copenhagen Ø, Denmark
| |
Collapse
|
20
|
Abstract
Damage to RNA from ultraviolet light, oxidation, chlorination, nitration, and akylation can include chemical modifications to nucleobases as well as RNA-RNA and RNA-protein crosslinking. In vitro studies have described a range of possible damage products, some of which are supported as physiologically relevant by in vivo observations in normal growth, stress conditions, or disease states. Damage to both messenger RNA and noncoding RNA may have functional consequences, and work has begun to elucidate the role of RNA turnover pathways and specific damage recognition pathways in clearing cells of these damaged RNAs.
Collapse
|
21
|
Zundel MA, Basturea GN, Deutscher MP. Initiation of ribosome degradation during starvation in Escherichia coli. RNA (NEW YORK, N.Y.) 2009; 15:977-83. [PMID: 19324965 PMCID: PMC2673067 DOI: 10.1261/rna.1381309] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Accepted: 02/10/2009] [Indexed: 05/22/2023]
Abstract
Ribosomes are known to be degraded under conditions of nutrient limitation. However, the mechanism by which a normally stable ribosome becomes a substrate for the degradation machinery has remained elusive. Here, we present in vitro and in vivo data demonstrating that free ribosome subunits are the actual targets of the degradative enzymes, whereas 70S particles are protected from such degradation. Conditions that increase the formation of subunits both in vitro and in vivo lead to enhanced degradation, while conditions favoring the presence of intact 70S ribosomes prevent or reduce breakdown. Thus, the simple formation of free 50S and 30S subunits is sufficient to serve as the initiation mechanism that allows endoribonuclease cleavage and subsequent ribosome breakdown.
Collapse
Affiliation(s)
- Michael A Zundel
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
| | | | | |
Collapse
|
22
|
Abstract
Ribosomal RNA transcription is the rate-limiting step in ribosome synthesis in bacteria and has been investigated intensely for over half a century. Multiple mechanisms ensure that rRNA synthesis rates are appropriate for the cell's particular growth condition. Recently, important advances have been made in our understanding of rRNA transcription initiation in Escherichia coli. These include (a) a model at the atomic level of the network of protein-DNA and protein-protein interactions that recruit RNA polymerase to rRNA promoters, accounting for their extraordinary strength; (b) discovery of the nonredundant roles of two small molecule effectors, ppGpp and the initiating NTP, in regulation of rRNA transcription initiation; and (c) identification of a new component of the transcription machinery, DksA, that is absolutely required for regulation of rRNA promoter activity. Together, these advances provide clues important for our molecular understanding not only of rRNA transcription, but also of transcription in general.
Collapse
Affiliation(s)
- Brian J Paul
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, USA.
| | | | | | | |
Collapse
|
23
|
Affiliation(s)
- Murray P Deutscher
- Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, Miami, Florida 33101, USA.
| |
Collapse
|
24
|
Murray HD, Schneider DA, Gourse RL. Control of rRNA expression by small molecules is dynamic and nonredundant. Mol Cell 2003; 12:125-34. [PMID: 12887898 DOI: 10.1016/s1097-2765(03)00266-1] [Citation(s) in RCA: 161] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The control of ribosomal RNA transcription is one of the most enduring issues in molecular microbiology, having been subjected to intense scrutiny for over 50 years. Rapid changes in rRNA expression occur during transitions in the bacterial growth cycle and following nutritional shifts during exponential growth. Genetic approaches and measurements of initiating nucleoside triphosphate (iNTP) and guanosine 5'-diphosphate, 3'-diphosphate (ppGpp) concentrations and of rRNA promoter activities showed that rapid changes in the concentrations of iNTPs and ppGpp account for the rapid changes in rRNA expression. The two regulatory signals are nonredundant: changes in iNTP concentration dominate regulation during outgrowth from stationary phase, whereas changes in ppGpp concentration are responsible for regulation following upshifts and downshifts during exponential phase. The results suggest a molecular logic for the use of two homeostatic regulatory mechanisms to monitor different aspects of ribosome activity and provide general insights into the nature of overlapping regulatory circuits.
Collapse
Affiliation(s)
- Heath D Murray
- Department of Bacteriology, University of Wisconsin, 420 Henry Mall, Madison, WI 53706, USA
| | | | | |
Collapse
|
25
|
Fegatella F, Lim J, Kjelleberg S, Cavicchioli R. Implications of rRNA operon copy number and ribosome content in the marine oligotrophic ultramicrobacterium Sphingomonas sp. strain RB2256. Appl Environ Microbiol 1998; 64:4433-8. [PMID: 9797303 PMCID: PMC106665 DOI: 10.1128/aem.64.11.4433-4438.1998] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/1998] [Accepted: 08/31/1998] [Indexed: 11/20/2022] Open
Abstract
Sphingomonas sp. strain RB2256 is a representative of the dominant class of ultramicrobacteria that are present in marine oligotrophic waters. In this study we examined the rRNA copy number and ribosome content of RB2256 to identify factors that may be associated with the relatively low rate of growth exhibited by the organism. It was found that RB2256 contains a single copy of the rRNA operon, in contrast to Vibrio spp., which contain more than eight copies. The maximum number of ribosomes per cell was observed during mid-log phase; however, this maximum content was low compared to those of faster-growing, heterotrophic bacteria (approximately 8% of the maximum ribosome content of Escherichia coli with a growth rate of 1. 5 h-1). The low number of ribosomes per cell appears to correlate with the low rate of growth (0.16 to 0.18 h-1) and the presence of a single copy of the rRNA operon. However, on the basis of cell volume, RB2256 appears to have a higher concentration of ribosomes than E. coli (approximately double that of E. coli with a growth rate of 1.5 h-1). Ribosome numbers reached maximum levels during mid-log-phase growth but decreased rapidly to 10% of maximum during late log phase through 7 days of starvation. The cells in late log phase and at the onset of starvation displayed an immediate response to a sudden addition of excess glucose (3 mM). This result demonstrates that a ribosome content 10% of maximum is sufficient to allow cells to immediately respond to nutrient upshift and achieve maximum rates of growth. These data indicate that the bulk of the ribosome pool is not required for protein synthesis and that ribosomes are not the limiting factor contributing to a low rate of growth. Our findings show that the regulation of ribosome content, the number of ribosomes per cell, and growth rate responses in RB2256 are fundamentally different from those characteristics in fast-growing heterotrophs like E. coli and that they may be characteristics typical of oligotrophic ultramicrobacteria.
Collapse
Affiliation(s)
- F Fegatella
- School of Microbiology and Immunology, The University of New South Wales, Sydney, 2052 New South Wales, Australia
| | | | | | | |
Collapse
|
26
|
Abstract
Proteins synthesized in Escherichia coli during recovery from starvation were resolved by two-dimensional polyacrylamide gel electrophoresis. Nine outgrowth-specific proteins, which appeared in two kinetic groups, that were not detected in either starved or exponential-phase cells were synthesized. Five other proteins whose rate of synthesis during outgrowth was > or = 5-fold higher than during exponential growth were observed.
Collapse
Affiliation(s)
- D A Siegele
- Department of Biology, Texas A&M University, College Station 77843-3258, USA.
| | | |
Collapse
|
27
|
Marouga R, Kjelleberg S. Synthesis of immediate upshift (Iup) proteins during recovery of marine Vibrio sp. strain S14 subjected to long-term carbon starvation. J Bacteriol 1996; 178:817-22. [PMID: 8550518 PMCID: PMC177730 DOI: 10.1128/jb.178.3.817-822.1996] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Proteins induced during the initial phase of recovery after long-term carbon starvation in the marine Vibrio sp. strain S14 were identified by two-dimensional gel electrophoresis analysis. Nutritional upshift experiments with pulse-labeled cells were performed after addition of glucose to cells starved for 48 h. Eighteen proteins synthesized during the first 3 min after substrate addition were identified and designated immediate upshift proteins (Iup proteins). They were induced at least 10-fold compared with the rate of synthesis during starvation. Of the Iup proteins, five are not found in exponentially growing cells. Subsequent to the first 3 min of glucose addition, a complex pattern of sequential synthesis of proteins made during a transient phase as well as proteins made during 60 min of the outgrowth response was monitored. To resolve whether the Iup proteins were synthesized from stable transcripts, the initiation of transcription was inhibited by rifampin (Rif). Addition of Rif 5 min prior to glucose promoted upshift resulted in the synthesis of 12 Iup proteins. Furthermore, three Iup proteins were still induced by cells that were Rif treated 20 min prior to the upshift. These results suggest that stable but silent transcripts exist during starvation and that the translation of these mRNA species is initiated by substrate addition. This regulatory mechanism may be essential for an immediate initiation of the recovery program by the nongrowing cell.
Collapse
Affiliation(s)
- R Marouga
- Department of General and Marine Microbiology, Göteborg University, Sweden
| | | |
Collapse
|
28
|
Flärdh K, Kjelleberg S. Glucose upshift of carbon-starved marine Vibrio sp. strain S14 causes amino acid starvation and induction of the stringent response. J Bacteriol 1994; 176:5897-903. [PMID: 7928949 PMCID: PMC196805 DOI: 10.1128/jb.176.19.5897-5903.1994] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The physiological status of carbon-starved cells of the marine Vibrio sp. strain S14 has been investigated by the analysis of their immediate response to carbon and energy sources. During the first minute after glucose addition to 48-h-starved cells, the pools of ATP and GTP increased rapidly, and the [ATP]/[ADP] ratio reached the level typical for growing cells within 4 min. The total rates of RNA and protein synthesis increased initially but were inhibited 4 to 5 min after glucose addition by the induction of the stringent response. A mutation in the relA gene abolished stringent control during the recovery and significantly prolonged the lag phase, before the starved cells regrew, after the addition of a single source of carbon. However, both the wild-type and the relA cells regrew without a significant lag phase when given glucose supplemented with amino acids. On the basis of these results, it is suggested that carbon-starved cells are deficient in amino acid biosynthesis and that ppGpp and the stringent response are involved in overcoming this deficiency, presumably by depressing the synthesis of amino acid biosynthetic enzymes. Furthermore, the data suggest that the starved cells primarily are starved for energy, and evidence is presented that the step-up in the rate of protein synthesis after refeeding is partially dependent on de novo RNA synthesis.
Collapse
Affiliation(s)
- K Flärdh
- Department of General and Marine Microbiology, Lundberg Laboratory, University of Göteborg, Sweden
| | | |
Collapse
|
29
|
Affiliation(s)
- U Wanner
- Swiss Federal Institute for Water Resources and Water Pollution Control, Swiss Federal Institutes of Technology, Dübendorf
| | | |
Collapse
|
30
|
Mink RW, Patterson JA, Hespell RB. Changes in Viability, Cell Composition, and Enzyme Levels During Starvation of Continuously Cultured (Ammonia-Limited)
Selenomonas ruminantium. Appl Environ Microbiol 1982; 44:913-22. [PMID: 16346116 PMCID: PMC242117 DOI: 10.1128/aem.44.4.913-922.1982] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Under nitrogen (ammonia)-limited continuous culture conditions, the ruminal anaerobe
Selenomonas ruminantium
was grown at various dilution rates (D). The proportion of the population that was viable increased with D, being 91% at D = 0.5 h
−1
. Washed cell suspensions were subjected to long-term nutrient starvation at 39°C. All populations exhibited logarithmic linear declines in viability that were related to the growth rate. Cells grown at D = 0.05, 0.20, and 0.50 lost about 50% viability after 8.1, 4.6, and 3.6 h, respectively. The linear rates of decline in total cell numbers were dramatically less and constant regardless of dilution rate. All major cell constituents declined during starvation, with the rates of decline being greatest with RNA, followed by DNA, carbohydrate, cell dry weight, and protein. The rates of RNA loss increased with cells grown at higher D values, whereas the opposite was observed for rates of carbohydrate losses. The majority of the degraded RNA was not catabolized but was excreted into the suspending buffer. At all D values,
S. ruminantium
produced mainly lactate and lesser amounts of acetate, propionate, and succinate during growth. With starvation, only small amounts of acetate were produced. Addition of glucose, vitamins, or both to the suspending buffer or starvation in the spent culture medium resulted in greater losses of viability than in buffer alone. Examination of extracts made from starving cells indicated that fructose diphosphate aldolase and lactate dehydrogenase activities remained relatively constant. Both urease and glutamate dehydrogenase activities declined gradually during starvation, whereas glutamine synthetase activity increased slightly. The data indicate that nitrogen (ammonia)-limited
S. ruminantium
cells have limited survival capacity, but this capacity is greater than that found previously with energy (glucose)-limited cells. Apparently no one cellular constituent serves as a catabolic substrate for endogenous metabolism. Relative to losses in viability, cellular enzymes are stable, indicating that nonviable cells maintain potential metabolic activity and that generalized, nonspecific enzyme degradation is not a major factor contributing to viability loss.
Collapse
Affiliation(s)
- R W Mink
- Department of Dairy Science, Microbiology Division, University of Illinois, Urbana, Illinois 61801
| | | | | |
Collapse
|
31
|
Batts-Young B, Lodish HF, Jacobson A. Similarity of the primary sequences of ribosomal RNAs isolated from vegetative and developing cells of Dictyostelium discoidem. Dev Biol 1980; 78:352-64. [PMID: 6773836 DOI: 10.1016/0012-1606(80)90340-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
32
|
Leal J. Effect of glucose starvation on the expression of transferred tsx genes in Escherichia coli K12 zygotes. MOLECULAR & GENERAL GENETICS : MGG 1976; 147:53-8. [PMID: 785225 DOI: 10.1007/bf00337935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Escherichia coli K12 Hfr H Tsxs Strs and F- Pro- Tsxr His- Arg- Strr bacteria were conjugated in the absence of arginine with or without glucose. The efficiency of conjugation, measured by the frequency of Pro+ and His+ recombinants was not affected. Arginine starvation alone did not affect the tsxs gene expression which occurred in all the zygotes which had received the gene. In contrast, argine and glucose starvation allows tsxs expression only in those zygotes in which the donor gene had been integrated in the genome. As the glucose starvation brings on a destabilization of the messenger RNA synthesized by the F- cells in absence of arginine, the results can be interpreted as follows: the transferred tsxs genes are transitorily expressed in all the zygotes at the unintegrated state. After this transient period, only thsoe genes integrated in the chromosomes of the zygotes continue to be expressed.
Collapse
|
33
|
Hwang LT, Giacomoni D. Synthesis of inducible enzyme in Escherichia coli recovering from prolonged energy starvation. BIOCHIMICA ET BIOPHYSICA ACTA 1976; 435:349-61. [PMID: 182224 DOI: 10.1016/0005-2787(76)90201-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A marked breakdown of ribosomes and rRNA occurs in Escherichia coli cells during prolonged deprivation of a carbon source (energy starvation). In E. coli recovering from energy starvation: (a) synthesis of RNA started immediately, total protein synthesis showed a delay of 5 to 10 minutes; (b) beta-galactosidase, tryptophanase and serine deaminase could not be induced in the first 50--70 min; (c) a lag of 60 min in the synthesis of beta-galactosidase was observed in a lac constitutive mutant of E. coli; synthesis of the constitutive enzyme malate dehydrogenase did not shown any delay. RNA synthesized in the early stages of recovery contained a higher percentage of low molecular weight molecules than RNA synthesized after 70 min of recovery or during exponential growth. Messenger RNA specific for beta-galactosidase was not synthesized for the first 50--60 min of recovery even when the specific inducer was added to the cultures.
Collapse
|
34
|
Webb SJ. Genetic continuity and metabolic regulation as seen by the effects of various microwave and black light frequencies on these phenomena. Ann N Y Acad Sci 1975; 247:327-51. [PMID: 1090232 DOI: 10.1111/j.1749-6632.1975.tb36009.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
35
|
Hespell RB, Thomashow MF, Rittenberg SC. Changes in cell composition and viability of Bdellovibrio bacteriovorus during starvation. Arch Microbiol 1974; 97:313-27. [PMID: 4599992 DOI: 10.1007/bf00403070] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
36
|
Soffer RL, Savage M. A mutant of Escherichia coli defective in leucyl, phenylalanyl-tRNA-protein transferase. Proc Natl Acad Sci U S A 1974; 71:1004-7. [PMID: 4595564 PMCID: PMC388146 DOI: 10.1073/pnas.71.3.1004] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
A mutant of E. coli that lacks leucyl,-phenylalanyl-tRNA-protein transferase (EC 2.3.2.6) has been isolated. Ability to produce the two activities could be introduced into the mutant from an F' strain whose episome contains genetic material located between 45 and 54 min on the E. coli chromosome. When grown into stationary phase and resuspended in minimal medium with glycerol, the mutant exhibited a marked lag before resuming growth. Revertants that did not show this lag were selected and were found to have regained both transfer activities. Extracts of wild-type, mutant, and revertant strains were compared as acceptors for the enzymatic transfer of radioactive phenylalanine. Analysis of the labeled polypeptides by disc gel electrophoresis indicated that certain potential acceptors may be preferentially acylated in vivo. These data provide genetic confirmation that the same enzyme protein catalyzes the transfer of leucine and phenylalanine and suggest that leucyl,phenylalanyl-tRNA-protein transferase is involved in a growth regulatory mechanism.
Collapse
|
37
|
Gillespie D, Jacobson A, Gillespie S, Patterson D. Use of exhaustive nucleic acid hybridization for determining the amount and size distribution of newly synthesized bacterial message RNA. Biochem Genet 1973; 10:175-90. [PMID: 4584391 DOI: 10.1007/bf00485764] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
38
|
Patterson D, Gillespie D. Deductive analysis of a protein-synthesis mutant of Escherichia coli. Biochem Genet 1973; 8:205-30. [PMID: 4570566 DOI: 10.1007/bf00485547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
39
|
Saxinger WC, Ponnamperuma C, Gillespie D. Nucleic acid hybridization with RNA immobilized on filter paper. Proc Natl Acad Sci U S A 1972; 69:2975-8. [PMID: 4562748 PMCID: PMC389687 DOI: 10.1073/pnas.69.10.2975] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
RNA has been immobilized in a manner suitable for use in molecular hybridization experiments with dissolved RNA or DNA by a nonaqueous solid-phase reaction with carbonyldiimidazole and RNA "dry coated" on cellulose or, preferably, on previously activated phosphocellulose filters. Immobilization of RNA does not appear to alter its chemical character or cause it to acquire affinity for unspecific RNA or DNA. The versatility and efficiency of this method make it potentially attractive for use in routine analytical or preparative hybridization experiments, among other applications.
Collapse
|
40
|
Patterson D, Weinstein M, Marshall S, Gillespie D. A new RNA synthesis mutant of E. coli. Biochem Genet 1971; 5:563-78. [PMID: 5000592 DOI: 10.1007/bf00485674] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
41
|
Ribonucleic acid-deoxyribonucleic acid hybridization in aqueous solutions and in solutions containing formamide. Biochem J 1971; 125:481-7. [PMID: 4947395 PMCID: PMC1178082 DOI: 10.1042/bj1250481] [Citation(s) in RCA: 87] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Hybridization in 6xSSC (SSC, 0.15m-sodium chloride-0.015m-sodium citrate) at 66 degrees C was compared with hybridization in formamide-6xSSC (1:1, v/v) at 35 degrees C. As expected, the RNA hybridization potential was labile in the former system and stable in the latter. DNA retention by filters was poor in the formamide system, but could be improved. Several other properties of the hybridization reaction were explored and it was concluded that the formamide system is generally superior.
Collapse
|
42
|
Webb SJ, Rokosh DA. The influence of nutrition on the DNA content of Escherichia coli and its response to ultraviolet light. Photochem Photobiol 1971; 14:493-508. [PMID: 4941977 DOI: 10.1111/j.1751-1097.1971.tb06188.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
43
|
Hodson RC, Schiff JA. Studies of sulfate utilization by algae: 8. The ubiquity of sulfate reduction to thiosulfate. PLANT PHYSIOLOGY 1971; 47:296-9. [PMID: 16657611 PMCID: PMC365857 DOI: 10.1104/pp.47.2.296] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Cell-free extracts from several microorganisms, when prepared by methods originally devised for Chlorella pyrenoidosa (Emerson strain 3) and incubated anaerobically with ATP, Mg(2+), and 2, 3-dimercaptopropan-1-ol, are capable of reducing sulfate-(35)S to thiosulfate. These microorganisms include, in addition to C. pyrenoidosa (Emerson strain 3), several other strains of C. pyrenoidosa, Chlorella protothecoides, Chlorella vulgaris, Anacystis sp., Chlamydomonas reinhardi, Escherichia coli, Salmonella typhimurium, and baker's yeast. Three of these organisms, E. coli, S. typhimurium, and baker's yeast, were previously reported by others to reduce sulfate to sulfite. Moreover, three mutant strains of S. typhimurium (Ba-25, Ce-363, and Bc-482) previously reported by other workers to be unable to reduce sulfate to sulfite also cannot form thiosulfate, and one mutant strain (Cd-68) reportedly able to form sulfite can also form thiosulfate. Taken together, this suggests that thiosulfate-forming activity may be a common feature of sulfate-reducing systems, and it may be present in enzymatic systems previously thought to be forming sulfite. Reasonably conclusive identification of thiosulfate is provided by ion exchange chromatography and by paper electrophoresis; the ambiguities associated with other analytical methods are discussed.
Collapse
Affiliation(s)
- R C Hodson
- Department of Biology, Brandeis University, Waltham, Massachusetts 02154
| | | |
Collapse
|
44
|
Boylen CW, Ensign JC. Intracellular substrates for endogenous metabolism during long-term starvation of rod and spherical cells of Arthrobacter crystallopoietes. J Bacteriol 1970; 103:578-87. [PMID: 5474876 PMCID: PMC248129 DOI: 10.1128/jb.103.3.578-587.1970] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Cells of Arthrobacter crystallopoietes, harvested during growth as spheres and as rods, were starved by shaking at 30 C in phosphate buffer for 30 days, during which time they maintained 100% viability. Changes in cellular components and the activity of specific enzyme pathways were monitored. A glycogen-like polysaccharide comprised 40% of the dry weight of growing spherical cells and 10% of the dry weight of rod cells. This material was utilized at approximately the same rate, on a percentage basis, during starvation of both cell forms. The rods degraded intracellular protein at approximately twice the rate of the spheres. At the end of 30 days, the rods had degraded 40% and the spheres 20% of their initial content of protein. Ribonucleic acid (RNA) was degraded significantly more rapidly in the rods. After 30 days starvation, 85 and 32% of the initial RNA of rods and spheres, respectively, had been depleted. Magnesium ion followed this same general pattern; the rods lost 65% and the spheres 45% of their initial content during 28 days of starvation. Deoxyribonucleic acid increased by 20% during the first few hours of starvation of both cell forms and then remained constant. The ability of glucose-, succinate-, and 2-hydroxypyridine (2-HP)-grown cells to oxidize glucose remained constant during 14 days of starvation. The ability of succinate-grown cells to oxidize succinate decreased rapidly during the first few hours of starvation to a rate which remained constant for 14 days. Cells adapted to growth on 2-HP completely lost their ability to oxidize this substrate after 3 days starvation.
Collapse
|
45
|
Ensign JC. Long-term starvation survival of rod and spherical cells of Arthrobacter crystallopoietes. J Bacteriol 1970; 103:569-77. [PMID: 4919984 PMCID: PMC248128 DOI: 10.1128/jb.103.3.569-577.1970] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Spherical and rod-shaped cells of Arthrobacter crystallopoietes, harvested during exponential growth, were subjected to total starvation for periods of time as long as 80 days. Viability measurements were made by plate count and slide culture procedures. Both cell forms remained 100% viable for 30 days. Thereafter, viability of rods and spheres decreased equally at a slow rate. After 60 days of starvation, more than 65% of both cell forms were viable. No significant cell lysis occurred as evidenced by microscopic examination, the small amount of 260-nm absorbing material found in the starvation buffer, and stability of radioactively labeled deoxyribonucleic acid in the cells. Endogenous respiration decreased 80-fold during the first 2 days of starvation, accompanied by a 30% decrease in dry weight of the cells. Thereafter, cellular carbon was oxidized to CO(2) at the constant level of 0.03%/hr over the remaining 78-day starvation period.
Collapse
|
46
|
Patterson D, Weinstein M, Nixon R, Gillespie D. Interaction of ribosomes and the cell envelope of Escherichia coli mediated by lysozyme. J Bacteriol 1970; 101:584-91. [PMID: 4905312 PMCID: PMC284944 DOI: 10.1128/jb.101.2.584-591.1970] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Evidence is presented suggesting the existence of a natural ribosome-membrane complex. A reconstruction system is described wherein free ribosomes form a complex which appears to involve cell fragments. The reconstructed complex is similar in stability to the inferred natural complex. The reconstructed complex is generated by lysozyme, and it is concluded that at least part of the inferred natural complex is also generated by lysozyme. These results are discussed with reference to existing data concerning certain membrane-associated systems in bacteria.
Collapse
|
47
|
Bleecken S. [The duplification system of the bacterial cell. II. Relations between DNA replication and cell division during transition between steady states of growth]. ZEITSCHRIFT FUR ALLGEMEINE MIKROBIOLOGIE 1969; 9:499-530. [PMID: 4911347 DOI: 10.1002/jobm.3630090702] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
48
|
Boyd D, Nixon R, Gillespie S, Gillespie D. Screening of Escherichia coli temperature-sensitive mutants by pretreatment with glucose starvation. J Bacteriol 1968; 95:1040-50. [PMID: 4868351 PMCID: PMC252129 DOI: 10.1128/jb.95.3.1040-1050.1968] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A system for screening Escherichia coli temperature-sensitive mutants is described. The system involves glucose starvation and minimizes ambiguities introduced by the interdependencies of macromolecular synthesis during balanced growth. The system permits the quick recognition of protein synthesis mutants and their classification into two general catagories. Complete protein synthesis mutants are unable to make any polypeptide material, whereas partial protein synthesis mutants are able to produce inactive proteins. The phenotypes of several mutants are described.
Collapse
|