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Wang T, Chen Q, Liang Q, Zhao Q, Lu X, Tian J, Guan Z, Liu C, Li J, Zhou M, Tian J, Liang C. Bacillus suppresses nitrogen efficiency of soybean-rhizobium symbiosis through regulation of nitrogen-related transcriptional and microbial patterns. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38963088 DOI: 10.1111/pce.15023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/21/2024] [Accepted: 06/21/2024] [Indexed: 07/05/2024]
Abstract
The regulation of legume-rhizobia symbiosis by microorganisms has obtained considerable interest in recent research, particularly in the common rhizobacteria Bacillus. However, few studies have provided detailed explanations regarding the regulatory mechanisms involved. Here, we investigated the effects of Bacillus (Bac.B) on Bradyrhizobium-soybean (Glycine max) symbiosis and elucidated the underlying ecological mechanisms. We found that two Bradyrhizobium strains (i.e. Bra.Q2 and Bra.D) isolated from nodules significantly promoted nitrogen (N) efficiency of soybean via facilitating nodule formation, thereby enhanced plant growth and yield. However, the intrusion of Bac.B caused a reverse shift in the synergistic efficiency of N2 fixation in the soybean-Bradyrhizobium symbiosis. Biofilm formation and naringenin may be importantin suppression of Bra.Q2 growth regulated by Bac.B. In addition, transcriptome and microbiome analyses revealed that Bra.Q2 and Bac.B might interact to regulateN transport and assimilation, thus influence the bacterial composition related to plant N nutrition in nodules. Also, the metabolisms of secondary metabolites and hormones associated with plant-microbe interaction and growth regulation were modulated by Bra.Q2 and Bac.B coinoculation. Collectively, we demonstrate that Bacillus negatively affects Bradyrhizobium-soybean symbiosis and modulate microbial interactions in the nodule. Our findings highlight a novel Bacillus-based regulation to improve N efficiency and sustainable agricultural development.
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Affiliation(s)
- Tianqi Wang
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Qianqian Chen
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Quan Liang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Qian Zhao
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Xing Lu
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Jihui Tian
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Zidi Guan
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Chang Liu
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Jifu Li
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Ming Zhou
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Jiang Tian
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Cuiyue Liang
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
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2
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Root-Bernstein RS, Bernstein MI. 'Evolutionary poker': an agent-based model of interactome emergence and epistasis tested against Lenski's long-term E. coli experiments. J Physiol 2024; 602:2511-2535. [PMID: 37707489 DOI: 10.1113/jp284421] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/23/2023] [Indexed: 09/15/2023] Open
Abstract
A simple agent-based model is presented that produces results matching the experimental data found by Lenski's group for ≤50,000 generations of Escherichia coli bacteria under continuous selective pressure. Although various mathematical models have been devised previously to model the Lenski data, the present model has advantages in terms of overall simplicity and conceptual accessibility. The model also clearly illustrates a number of features of the evolutionary process that are otherwise not obvious, such as the roles of epistasis and historical contingency in adaptation and why evolution is time irreversible ('Dollo's law'). The reason for this irreversibility is that genomes become increasingly integrated or organized, and this organization becomes a novel selective factor itself, against which future generations must compete. Selection for integrated or synergistic networks, systems or sets of mutations or traits, not for individual mutations, confers the main adaptive advantage. The result is a punctuated form of evolution that follows a logarithmic occurrence probability, in which evolution proceeds very quickly when interactomes begin to form but which slows as interactomes become more robust and the difficulty of integrating new mutations increases. Sufficient parameters exist in the game to suggest not only how equilibrium or stasis is reached but also the conditions in which it will be punctuated, the factors governing the rate at which genomic organization occurs and novel traits appear, and how population size, genome size and gene variability affect these.
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Affiliation(s)
| | - Morton I Bernstein
- Department of Physiology, Michigan State University, East Lansing, MI, USA
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3
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Mahesh S, Carmelin DS, Muthusamy R. Bacterial Flora and Treatment Strategies in Women With Escherichia coli Urinary Tract Infections. Cureus 2024; 16:e56552. [PMID: 38646229 PMCID: PMC11027953 DOI: 10.7759/cureus.56552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/20/2024] [Indexed: 04/23/2024] Open
Abstract
Introduction This study explores the intricate relationship between bacterial flora and the occurrence of Escherichia coli (E. coli) infections in gynecological patients. It aims to provide insights into the various treatment strategies used to effectively manage bacterial pathogens, especially E. coli infections. By conducting a comprehensive analysis of the bacterial flora in gynecological patients, the study highlights the notable presence of E. coli, prompting further investigation into the factors that contribute to its colonization. The objective of the study is to comprehensively investigate and detect urinary tract infections (UTIs) specifically caused by E. coli among gynecological patients. The study aims to delve into bacterial flora prevalence, antibiotic resistance patterns, and potential virulence factors. Through this analysis, the study intends to identify effective strategies for rapid detection and diagnosis of UTIs caused by E. coli by utilizing advanced microbiological and molecular techniques. Furthermore, the study aims to formulate and propose a strategic treatment approach with a particular emphasis on selecting appropriate antibiotics to reduce the risk of severe infections and associated complications. Materials and methods The methodology employed in this study included the isolation and characterization of bacterial strains from clinical samples obtained from gynecological patients. A total of 52 urine specimens were collected from patients with complaints of infection in the urinary tract and infertility. These samples underwent both preliminary and confirmatory microbiological analysis, such as gram staining, biochemical confirmation test, and antibiotic susceptibility, and further proceeded with the multiplex polymerase chain reaction (PCR) technique. The results of PCR and antibiotic susceptibility revealed the specific gene involvement and resistant characteristics of E. coli. Results The findings revealed a total of 32 specimens positive for E. coli, of which 10 patients had infertility complaints and 22 patients had UTIs. The preliminary test, gram staining, showed the gram-negative bacilli E. coli, and the nutrient agar plate revealed smooth circular translucent colonies; MacConkey agar showed pink-colored lactose-fermented colonies; and the blood and chocolate agar plates showed grayish white moist gamma-hemolytic colonies. The biochemical confirmation of E. coli resulted in positive for indole and methyl red tests and negative for Voges-Proskauer and citrate utilization tests. The multiplex PCR analysis confirmed the E. coli strains with the presence of two target genes, stx2d and stx2e. Conclusion To summarize, this study offers valuable insights into the bacterial flora of gynecological patients impacted by E. coli infections, which provides a foundation for the development of precise and efficient treatment strategies. The results emphasize the importance of personalized treatment approaches that consider both the microbiological characteristics of the infection and the evolving landscape of antibiotic resistance. The implication of this research extends to enhancing clinical outcomes and alleviating the burden of E. coli infections in gynecological settings.
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Affiliation(s)
- Saisri Mahesh
- Center for Global Health Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
| | - Durai Singh Carmelin
- Center for Global Health Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
| | - Raman Muthusamy
- Center for Global Health Research, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
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4
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Baverstock K. The Gene: An appraisal. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 186:e73-e88. [PMID: 38044248 DOI: 10.1016/j.pbiomolbio.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The gene can be described as the foundational concept of modern biology. As such, it has spilled over into daily discourse, yet it is acknowledged among biologists to be ill-defined. Here, following a short history of the gene, I analyse critically its role in inheritance, evolution, development, and morphogenesis. Wilhelm Johannsen's genotype-conception, formulated in 1910, has been adopted as the foundation stone of genetics, giving the gene a higher degree of prominence than is justified by the evidence. An analysis of the results of the Long-Term Evolution Experiment (LTEE) with E. coli bacteria, grown over 60,000 generations, does not support spontaneous gene mutation as the source of variance for natural selection. From this it follows that the gene is not Mendel's unit of inheritance: that must be Johannsen's transmission-conception at the gamete phenotype level, a form of inheritance that Johannsen did not consider. Alternatively, I contend that biology viewed on the bases of thermodynamics, complex system dynamics, and self-organisation, provides a new framework for the foundations of biology. In this framework, the gene plays a passive role as a vital information store: it is the phenotype that plays the active role in inheritance, evolution, development, and morphogenesis.
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Affiliation(s)
- Keith Baverstock
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio Campus, Kuopio, Finland.
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5
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Eng T, Banerjee D, Menasalvas J, Chen Y, Gin J, Choudhary H, Baidoo E, Chen JH, Ekman A, Kakumanu R, Diercks YL, Codik A, Larabell C, Gladden J, Simmons BA, Keasling JD, Petzold CJ, Mukhopadhyay A. Maximizing microbial bioproduction from sustainable carbon sources using iterative systems engineering. Cell Rep 2023; 42:113087. [PMID: 37665664 DOI: 10.1016/j.celrep.2023.113087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/10/2023] [Accepted: 08/18/2023] [Indexed: 09/06/2023] Open
Abstract
Maximizing the production of heterologous biomolecules is a complex problem that can be addressed with a systems-level understanding of cellular metabolism and regulation. Specifically, growth-coupling approaches can increase product titers and yields and also enhance production rates. However, implementing these methods for non-canonical carbon streams is challenging due to gaps in metabolic models. Over four design-build-test-learn cycles, we rewire Pseudomonas putida KT2440 for growth-coupled production of indigoidine from para-coumarate. We explore 4,114 potential growth-coupling solutions and refine one design through laboratory evolution and ensemble data-driven methods. The final growth-coupled strain produces 7.3 g/L indigoidine at 77% maximum theoretical yield in para-coumarate minimal medium. The iterative use of growth-coupling designs and functional genomics with experimental validation was highly effective and agnostic to specific hosts, carbon streams, and final products and thus generalizable across many systems.
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Affiliation(s)
- Thomas Eng
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Deepanwita Banerjee
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Javier Menasalvas
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yan Chen
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jennifer Gin
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hemant Choudhary
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA
| | - Edward Baidoo
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jian Hua Chen
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Axel Ekman
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ramu Kakumanu
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yuzhong Liu Diercks
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alex Codik
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Carolyn Larabell
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John Gladden
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA
| | - Blake A Simmons
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jay D Keasling
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; QB3 Institute, University of California, Berkeley, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608, USA; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, 2970 Horsholm, Denmark; Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Christopher J Petzold
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Aindrila Mukhopadhyay
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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6
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Brown OR, Hullender DA. Neo-Darwinism must Mutate to survive. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 172:24-38. [PMID: 35439500 DOI: 10.1016/j.pbiomolbio.2022.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 04/06/2022] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Abstract
Darwinian evolution is a nineteenth century descriptive concept that itself has evolved. Selection by survival of the fittest was a captivating idea. Microevolution was biologically and empirically verified by discovery of mutations. There has been limited progress to the modern synthesis. The central focus of this perspective is to provide evidence to document that selection based on survival of the fittest is insufficient for other than microevolution. Realistic probability calculations based on probabilities associated with microevolution are presented. However, macroevolution (required for all speciation events and the complexifications appearing in the Cambrian explosion) are shown to be probabilistically highly implausible (on the order of 10-50) when based on selection by survival of the fittest. We conclude that macroevolution via survival of the fittest is not salvageable by arguments for random genetic drift and other proposed mechanisms. Evolutionary biology is relevant to cancer mechanisms with significance beyond academics. We challenge evolutionary biology to advance boldly beyond the inadequacies of the modern synthesis toward a unifying theory modeled after the Grand Unified Theory in physics. This should include the possibility of a fifth force in nature. Mathematics should be rigorously applied to current and future evolutionary empirical discoveries. We present justification that molecular biology and biochemistry must evolve to aeon (life) chemistry that acknowledges the uniqueness of enzymes for life. To evolve, biological evolution must face the known deficiencies, especially the limitations of the concept survival of the fittest, and seek solutions in Eigen's concept of self-organization, Schrödinger's negentropy, and novel approaches.
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Affiliation(s)
- Olen R Brown
- Dalton Cardiovascular Research Center, University of Missouri- Columbia, USA.
| | - David A Hullender
- Professor of Mechanical and Aerospace Engineering at the University of Texas at Arlington, USA
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7
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Yanti NA. Phenotypic Characterization and Identification of Potential L-Asparaginase-Producing Thermohalophilic Bacteria from Wawolesea Hot Spring, North Konawe, Southeast Sulawesi, Indonesia. Pak J Biol Sci 2022; 25:1021-1032. [PMID: 36591934 DOI: 10.3923/pjbs.2022.1021.1032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
<b>Background and Objective:</b> L-asparaginase-producing thermohalophilic bacteria have the potential of producing an enzyme tolerant to high heat and salt levels. This enzyme, L-asparaginase, can be used as a biological agent for the cancer therapy of acute lymphoblastic leukemia and melanosarcoma as it has a specific ability to inhibit the formation of nutrients for cancer cells. This enzyme is also used effectively in food industries operating at high temperatures due to its ability to reduce acrylamide, a trigger of cancer cells. This study sought to figure out the phenotypic characters of and identify potential L-asparaginase-producing thermohalophilic bacteria from Wawolesea Hot Spring, North Konawe, Southeast Sulawesi. <b>Materials and Methods:</b> The characterization conducted on potential L-asparaginase-producing thermohalophilic bacterial isolates consisted of the following: Colony morphological characterization, covering the shapes, edges, internal structures, elevations and colours of the colonies, cell morphological characterization, covering gram staining, endospore formation and motility, biochemical characterization, covering catalase, Methyl Red and Voges Proskauer (MR-VP), gelatin hydrolysis, citrate, indole and carbohydrate fermentation tests and physiological characterization, covering pH effect, salinity, oxygen demand and temperature effect tests. Bacterial isolate identification was carried out in two stages, namely phenetic identification based on the phenotypic characterization data determine through a preliminary identification and numeric-phenetic identification. <b>Results:</b> The characterization results showed that the bacterial isolates AAT 1.4, AAT 3.2 and CAT 3.4 were <i>bacillus</i>-shaped, Gram-positive, motile, catalase-positive and aerobic. Based on the numeric-phenetic analysis results, the isolates AAT 1.4 and CAT 3.4 had a 92.9% similarity to <i>Bacillus subtilis</i>, while isolate AAT 3.2 had a 92.9% similarity to <i>Brevibacillus limnophilus</i>. <b>Conclusion:</b> According to the numeric-phenetic analysis results, the isolates AAT 1.4 and CAT 3.4 belong to the species <i>Bacillus subtilis</i>, while isolate AAT 3.2 belongs to the species <i>Brevibacillus limnophilus</i>.
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8
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Baverstock K. The gene: An appraisal. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 164:46-62. [PMID: 33979646 DOI: 10.1016/j.pbiomolbio.2021.04.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/14/2021] [Accepted: 04/22/2021] [Indexed: 11/29/2022]
Abstract
The gene can be described as the foundational concept of modern biology. As such, it has spilled over into daily discourse, yet it is acknowledged among biologists to be ill-defined. Here, following a short history of the gene, I analyse critically its role in inheritance, evolution, development, and morphogenesis. Wilhelm Johannsen's genotype-conception, formulated in 1910, has been adopted as the foundation stone of genetics, giving the gene a higher degree of prominence than is justified by the evidence. An analysis of the results of the Long-Term Evolution Experiment (LTEE) with E. coli bacteria, grown over 60,000 generations, does not support spontaneous gene mutation as the source of variance for natural selection. From this it follows that the gene is not Mendel's unit of inheritance: that must be Johannsen's transmission-conception at the gamete phenotype level, a form of inheritance that Johannsen did not consider. Alternatively, I contend that biology viewed on the bases of thermodynamics, complex system dynamics and self-organisation, provides a new framework for the foundations of biology. In this framework, the gene plays a passive role as a vital information store: it is the phenotype that plays the active role in inheritance, evolution, development, and morphogenesis.
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Affiliation(s)
- Keith Baverstock
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio Campus, Kuopio, Finland.
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9
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Abstract
Microbes are constantly evolving. Laboratory studies of bacterial evolution increase our understanding of evolutionary dynamics, identify adaptive changes, and answer important questions that impact human health. During bacterial infections in humans, however, the evolutionary parameters acting on infecting populations are likely to be much more complex than those that can be tested in the laboratory. Nonetheless, human infections can be thought of as naturally occurring in vivo bacterial evolution experiments, which can teach us about antibiotic resistance, pathogenesis, and transmission. Here, we review recent advances in the study of within-host bacterial evolution during human infection and discuss practical considerations for conducting such studies. We focus on 2 possible outcomes for de novo adaptive mutations, which we have termed "adapt-and-live" and "adapt-and-die." In the adapt-and-live scenario, a mutation is long lived, enabling its transmission on to other individuals, or the establishment of chronic infection. In the adapt-and-die scenario, a mutation is rapidly extinguished, either because it carries a substantial fitness cost, it arises within tissues that block transmission to new hosts, it is outcompeted by more fit clones, or the infection resolves. Adapt-and-die mutations can provide rich information about selection pressures in vivo, yet they can easily elude detection because they are short lived, may be more difficult to sample, or could be maladaptive in the long term. Understanding how bacteria adapt under each of these scenarios can reveal new insights about the basic biology of pathogenic microbes and could aid in the design of new translational approaches to combat bacterial infections.
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Affiliation(s)
- Matthew J. Culyba
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Daria Van Tyne
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
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10
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Castle LM, Schuh DA, Reynolds EE, Furst AL. Electrochemical Sensors to Detect Bacterial Foodborne Pathogens. ACS Sens 2021; 6:1717-1730. [PMID: 33955227 DOI: 10.1021/acssensors.1c00481] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacterial foodborne pathogens cause millions of illnesses each year and disproportionately impact those in developing countries. To combat these diseases and their spread, effective monitoring of foodborne pathogens is needed. Technologies to detect these microbes must be deployable at the point-of-contamination, often in nonideal environments. Electrochemical sensors are uniquely suited for field-deployable monitoring, as they are quantitative, rapid, and do not require expensive instrumentation. When combined with the inherent recognition capabilities of biomolecules, electrochemistry is unmatched for quantitative biological measurements with minimal equipment requirements. This Review is centered on recent advances in electrochemical sensors for the detection of bacterial foodborne pathogens with a specific emphasis on field-deployable platforms, as this is a key requirement of any technology that could effectively halt the spread of foodborne diseases. Innovative electrochemical sensing strategies are highlighted that demonstrate the ability of these technologies to achieve high sensitivity and large detection ranges with rapid readout. Sensing strategies are categorized on the basis of whether they incorporate biological pretreatments or biorecognition elements, and their key advantages and disadvantages are summarized. As this class of sensors continues to mature, methods to incorporate device specificity and to detect targets from complex solutions will enable the translation of these platforms from laboratory prototypes to real-world implementation.
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Affiliation(s)
- Lauren M. Castle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Daena A. Schuh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Erin E. Reynolds
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ariel L. Furst
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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11
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Rapid determination of sucrose and glucose in microbial fermentation and fruit juice samples using engineered multi-enzyme biosensing microchip. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106075] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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12
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Blount ZD, Maddamsetti R, Grant NA, Ahmed ST, Jagdish T, Baxter JA, Sommerfeld BA, Tillman A, Moore J, Slonczewski JL, Barrick JE, Lenski RE. Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment. eLife 2020; 9:55414. [PMID: 32469311 PMCID: PMC7299349 DOI: 10.7554/elife.55414] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/28/2020] [Indexed: 12/27/2022] Open
Abstract
Evolutionary innovations allow populations to colonize new ecological niches. We previously reported that aerobic growth on citrate (Cit+) evolved in an Escherichia coli population during adaptation to a minimal glucose medium containing citrate (DM25). Cit+ variants can also grow in citrate-only medium (DM0), a novel environment for E. coli. To study adaptation to this niche, we founded two sets of Cit+ populations and evolved them for 2500 generations in DM0 or DM25. The evolved lineages acquired numerous parallel mutations, many mediated by transposable elements. Several also evolved amplifications of regions containing the maeA gene. Unexpectedly, some evolved populations and clones show apparent declines in fitness. We also found evidence of substantial cell death in Cit+ clones. Our results thus demonstrate rapid trait refinement and adaptation to the new citrate niche, while also suggesting a recalcitrant mismatch between E. coli physiology and growth on citrate.
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Affiliation(s)
- Zachary D Blount
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States.,The BEACON Center for the Study of Evolution in Action, East Lansing, United States
| | - Rohan Maddamsetti
- Department of Biomedical Engineering, Duke University, Durham, United States
| | - Nkrumah A Grant
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States.,The BEACON Center for the Study of Evolution in Action, East Lansing, United States
| | - Sumaya T Ahmed
- Department of Biology, Kenyon College, Gambier, United States
| | - Tanush Jagdish
- The BEACON Center for the Study of Evolution in Action, East Lansing, United States.,Program for Systems, Synthetic, and Quantitative Biology, Harvard University, Cambridge, United States
| | - Jessica A Baxter
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States
| | - Brooke A Sommerfeld
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States
| | - Alice Tillman
- Department of Biology, Kenyon College, Gambier, United States
| | - Jeremy Moore
- Department of Biology, Kenyon College, Gambier, United States
| | | | - Jeffrey E Barrick
- The BEACON Center for the Study of Evolution in Action, East Lansing, United States.,Department of Molecular Biosciences, The University of Texas, Austin, United States
| | - Richard E Lenski
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States.,The BEACON Center for the Study of Evolution in Action, East Lansing, United States
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13
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Ye CJ, Stilgenbauer L, Moy A, Liu G, Heng HH. What Is Karyotype Coding and Why Is Genomic Topology Important for Cancer and Evolution? Front Genet 2019; 10:1082. [PMID: 31737054 PMCID: PMC6838208 DOI: 10.3389/fgene.2019.01082] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/09/2019] [Indexed: 12/14/2022] Open
Abstract
While the importance of chromosomal/nuclear variations vs. gene mutations in diseases is becoming more appreciated, less is known about its genomic basis. Traditionally, chromosomes are considered the carriers of genes, and genes define bio-inheritance. In recent years, the gene-centric concept has been challenged by the surprising data of various sequencing projects. The genome system theory has been introduced to offer an alternative framework. One of the key concepts of the genome system theory is karyotype or chromosomal coding: chromosome sets function as gene organizers, and the genomic topologies provide a context for regulating gene expression and function. In other words, the interaction of individual genes, defined by genomic topology, is part of the full informational system. The genes define the “parts inheritance,” while the karyotype and genomic topology (the physical relationship of genes within a three-dimensional nucleus) plus the gene content defines “system inheritance.” In this mini-review, the concept of karyotype or chromosomal coding will be briefly discussed, including: 1) the rationale for searching for new genomic inheritance, 2) chromosomal or karyotype coding (hypothesis, model, and its predictions), and 3) the significance and evidence of chromosomal coding (maintaining and changing the system inheritance-defined bio-systems). This mini-review aims to provide a new conceptual framework for appreciating the genome organization-based information package and its ultimate importance for future genomic and evolutionary studies.
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Affiliation(s)
- Christine J Ye
- The Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Lukas Stilgenbauer
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI, United States
| | - Amanda Moy
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI, United States
| | - Guo Liu
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI, United States
| | - Henry H Heng
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI, United States.,Department of Pathology, Wayne State University School of Medicine, Detroit, MI, United States
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14
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Li Z, Bock R. Rapid functional activation of a horizontally transferred eukaryotic gene in a bacterial genome in the absence of selection. Nucleic Acids Res 2019; 47:6351-6359. [PMID: 31106341 PMCID: PMC6614815 DOI: 10.1093/nar/gkz370] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/07/2019] [Accepted: 04/30/2019] [Indexed: 12/02/2022] Open
Abstract
Horizontal gene transfer has occurred between organisms of all domains of life and contributed substantially to genome evolution in both prokaryotes and eukaryotes. Phylogenetic evidence suggests that eukaryotic genes horizontally transferred to bacteria provided useful new gene functions that improved metabolic plasticity and facilitated adaptation to new environments. How these eukaryotic genes evolved into functional bacterial genes is not known. Here, we have conducted a genetic screen to identify the mechanisms involved in functional activation of a eukaryotic gene after its transfer into a bacterial genome. We integrated a eukaryotic selectable marker gene cassette driven by expression elements from the red alga Porphyridium purpureum into the genome of Escherichia coli. Following growth under non-selective conditions, gene activation events were indentified by antibiotic selection. We show that gene activation in the bacterial recipient occurs at high frequency and involves two major types of spontaneous mutations: deletion and gene amplification. We further show that both mechanisms result in promoter capture and are frequently triggered by microhomology-mediated recombination. Our data suggest that horizontally transferred genes have a high probability of acquiring functionality, resulting in their maintenance if they confer a selective advantage.
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Affiliation(s)
- Zhichao Li
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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15
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Shapiro JA. No genome is an island: toward a 21st century agenda for evolution. Ann N Y Acad Sci 2019; 1447:21-52. [DOI: 10.1111/nyas.14044] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/17/2019] [Accepted: 02/02/2019] [Indexed: 12/21/2022]
Affiliation(s)
- James A. Shapiro
- Department of Biochemistry and Molecular BiologyUniversity of Chicago Chicago Illinois
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16
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Blount ZD, Lenski RE, Losos JB. Contingency and determinism in evolution: Replaying life’s tape. Science 2018; 362:362/6415/eaam5979. [DOI: 10.1126/science.aam5979] [Citation(s) in RCA: 263] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Historical processes display some degree of “contingency,” meaning their outcomes are sensitive to seemingly inconsequential events that can fundamentally change the future. Contingency is what makes historical outcomes unpredictable. Unlike many other natural phenomena, evolution is a historical process. Evolutionary change is often driven by the deterministic force of natural selection, but natural selection works upon variation that arises unpredictably through time by random mutation, and even beneficial mutations can be lost by chance through genetic drift. Moreover, evolution has taken place within a planetary environment with a particular history of its own. This tension between determinism and contingency makes evolutionary biology a kind of hybrid between science and history. While philosophers of science examine the nuances of contingency, biologists have performed many empirical studies of evolutionary repeatability and contingency. Here, we review the experimental and comparative evidence from these studies. Replicate populations in evolutionary “replay” experiments often show parallel changes, especially in overall performance, although idiosyncratic outcomes show that the particulars of a lineage’s history can affect which of several evolutionary paths is taken. Comparative biologists have found many notable examples of convergent adaptation to similar conditions, but quantification of how frequently such convergence occurs is difficult. On balance, the evidence indicates that evolution tends to be surprisingly repeatable among closely related lineages, but disparate outcomes become more likely as the footprint of history grows deeper. Ongoing research on the structure of adaptive landscapes is providing additional insight into the interplay of fate and chance in the evolutionary process.
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Affiliation(s)
- Zachary D. Blount
- Department of Microbiology and Molecular Genetics and BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824, USA
- Department of Biology, Kenyon College, Gambier, OH 43022, USA
| | - Richard E. Lenski
- Department of Microbiology and Molecular Genetics and BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824, USA
| | - Jonathan B. Losos
- Department of Biology, Washington University, St. Louis, MO 63130, USA
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17
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Eng T, Demling P, Herbert RA, Chen Y, Benites V, Martin J, Lipzen A, Baidoo EEK, Blank LM, Petzold CJ, Mukhopadhyay A. Restoration of biofuel production levels and increased tolerance under ionic liquid stress is enabled by a mutation in the essential Escherichia coli gene cydC. Microb Cell Fact 2018; 17:159. [PMID: 30296937 PMCID: PMC6174563 DOI: 10.1186/s12934-018-1006-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/26/2018] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Microbial production of chemicals from renewable carbon sources enables a sustainable route to many bioproducts. Sugar streams, such as those derived from biomass pretreated with ionic liquids (IL), provide efficiently derived and cost-competitive starting materials. A limitation to this approach is that residual ILs in the pretreated sugar source can be inhibitory to microbial growth and impair expression of the desired biosynthetic pathway. RESULTS We utilized laboratory evolution to select Escherichia coli strains capable of robust growth in the presence of the IL, 1-ethyl-3-methyl-imidizolium acetate ([EMIM]OAc). Whole genome sequencing of the evolved strain identified a point mutation in an essential gene, cydC, which confers tolerance to two different classes of ILs at concentrations that are otherwise growth inhibitory. This mutation, cydC-D86G, fully restores the specific production of the bio-jet fuel candidate D-limonene, as well as the biogasoline and platform chemical isopentenol, in growth medium containing ILs. Similar amino acids at this position in cydC, such as cydC-D86V, also confer tolerance to [EMIM]OAc. We show that this [EMIM]OAc tolerance phenotype of cydC-D86G strains is independent of its wild-type function in activating the cytochrome bd-I respiratory complex. Using shotgun proteomics, we characterized the underlying differential cellular responses altered in this mutant. While wild-type E. coli cannot produce detectable amounts of either product in the presence of ILs at levels expected to be residual in sugars from pretreated biomass, the engineered cydC-D86G strains produce over 200 mg/L D-limonene and 350 mg/L isopentenol, which are among the highest reported titers in the presence of [EMIM]OAc. CONCLUSIONS The optimized strains in this study produce high titers of two candidate biofuels and bioproducts under IL stress. Both sets of production strains surpass production titers from other IL tolerant mutants in the literature. Our application of laboratory evolution identified a gain of function mutation in an essential gene, which is unusual in comparison to other published IL tolerant mutants.
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Affiliation(s)
- Thomas Eng
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
| | - Philipp Demling
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, 52074 Aachen, Germany
| | - Robin A. Herbert
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
| | - Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
| | - Veronica Benites
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
| | - Joel Martin
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, 94598 USA
| | - Anna Lipzen
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, 94598 USA
| | - Edward E. K. Baidoo
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
| | - Lars M. Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, 52074 Aachen, Germany
| | - Christopher J. Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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18
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Van den Bergh B, Swings T, Fauvart M, Michiels J. Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution. Microbiol Mol Biol Rev 2018; 82:e00008-18. [PMID: 30045954 PMCID: PMC6094045 DOI: 10.1128/mmbr.00008-18] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.
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Affiliation(s)
- Bram Van den Bergh
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- Douglas Lab, Department of Entomology, Cornell University, Ithaca, New York, USA
| | - Toon Swings
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
| | - Maarten Fauvart
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- imec, Leuven, Belgium
| | - Jan Michiels
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
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19
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Tumen-Velasquez M, Johnson CW, Ahmed A, Dominick G, Fulk EM, Khanna P, Lee SA, Schmidt AL, Linger JG, Eiteman MA, Beckham GT, Neidle EL. Accelerating pathway evolution by increasing the gene dosage of chromosomal segments. Proc Natl Acad Sci U S A 2018; 115:7105-7110. [PMID: 29915086 PMCID: PMC6142232 DOI: 10.1073/pnas.1803745115] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Experimental evolution is a critical tool in many disciplines, including metabolic engineering and synthetic biology. However, current methods rely on the chance occurrence of a key step that can dramatically accelerate evolution in natural systems, namely increased gene dosage. Our studies sought to induce the targeted amplification of chromosomal segments to facilitate rapid evolution. Since increased gene dosage confers novel phenotypes and genetic redundancy, we developed a method, Evolution by Amplification and Synthetic Biology (EASy), to create tandem arrays of chromosomal regions. In Acinetobacter baylyi, EASy was demonstrated on an important bioenergy problem, the catabolism of lignin-derived aromatic compounds. The initial focus on guaiacol (2-methoxyphenol), a common lignin degradation product, led to the discovery of Amycolatopsis genes (gcoAB) encoding a cytochrome P450 enzyme that converts guaiacol to catechol. However, chromosomal integration of gcoAB in Pseudomonas putida or A. baylyi did not enable guaiacol to be used as the sole carbon source despite catechol being a growth substrate. In ∼1,000 generations, EASy yielded alleles that in single chromosomal copy confer growth on guaiacol. Different variants emerged, including fusions between GcoA and CatA (catechol 1,2-dioxygenase). This study illustrates the power of harnessing chromosomal gene amplification to accelerate the evolution of desirable traits.
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Affiliation(s)
| | | | - Alaa Ahmed
- Department of Microbiology, University of Georgia, Athens, GA 30602
| | - Graham Dominick
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401
| | - Emily M Fulk
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401
| | - Payal Khanna
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401
| | - Sarah A Lee
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA 30602
| | - Alicia L Schmidt
- Department of Microbiology, University of Georgia, Athens, GA 30602
| | - Jeffrey G Linger
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401
| | - Mark A Eiteman
- Department of Microbiology, University of Georgia, Athens, GA 30602
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA 30602
| | - Gregg T Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401;
| | - Ellen L Neidle
- Department of Microbiology, University of Georgia, Athens, GA 30602;
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20
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Leon D, D'Alton S, Quandt EM, Barrick JE. Innovation in an E. coli evolution experiment is contingent on maintaining adaptive potential until competition subsides. PLoS Genet 2018; 14:e1007348. [PMID: 29649242 PMCID: PMC5918244 DOI: 10.1371/journal.pgen.1007348] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/24/2018] [Accepted: 03/30/2018] [Indexed: 11/19/2022] Open
Abstract
Key innovations are disruptive evolutionary events that enable a species to escape constraints and rapidly diversify. After 15 years of the Lenski long-term evolution experiment with Escherichia coli, cells in one of the twelve populations evolved the ability to utilize citrate, an abundant but previously untapped carbon source in the environment. Descendants of these cells became dominant in the population and subsequently diversified as a consequence of invading this vacant niche. Mutations responsible for the appearance of rudimentary citrate utilization and for refining this ability have been characterized. However, the complete nature of the genetic and/or ecological events that set the stage for this key innovation is unknown. In particular, it is unclear why it took so long for citrate utilization to evolve and why it still has evolved in only one of the twelve E. coli populations after 30 years of the Lenski experiment. In this study, we recapitulated the initial mutation needed to evolve citrate utilization in strains isolated from throughout the first 31,500 generations of the history of this population. We found that there was already a slight fitness benefit for this mutation in the original ancestor of the evolution experiment and in other early isolates. However, evolution of citrate utilization was blocked at this point due to competition with other mutations that improved fitness in the original niche. Subsequently, an anti-potentiated genetic background evolved in which it was deleterious to evolve rudimentary citrate utilization. Only later, after further mutations accumulated that restored the benefit of this first-step mutation and the overall rate of adaptation in the population slowed, was citrate utilization likely to evolve. Thus, intense competition and the types of mutations that it favors can lead to short-sighted evolutionary trajectories that hide a stepping stone needed to access a key innovation from many future generations.
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Affiliation(s)
- Dacia Leon
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Simon D'Alton
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Erik M. Quandt
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Jeffrey E. Barrick
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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21
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Freddolino PL, Yang J, Momen-Roknabadi A, Tavazoie S. Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry. eLife 2018; 7:e31867. [PMID: 29620524 PMCID: PMC5919758 DOI: 10.7554/elife.31867] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 04/04/2018] [Indexed: 12/12/2022] Open
Abstract
Cells adapt to familiar changes in their environment by activating predefined regulatory programs that establish adaptive gene expression states. These hard-wired pathways, however, may be inadequate for adaptation to environments never encountered before. Here, we reveal evidence for an alternative mode of gene regulation that enables adaptation to adverse conditions without relying on external sensory information or genetically predetermined cis-regulation. Instead, individual genes achieve optimal expression levels through a stochastic search for improved fitness. By focusing on improving the overall health of the cell, the proposed stochastic tuning mechanism discovers global gene expression states that are fundamentally new and yet optimized for novel environments. We provide experimental evidence for stochastic tuning in the adaptation of Saccharomyces cerevisiae to laboratory-engineered environments that are foreign to its native gene-regulatory network. Stochastic tuning operates locally at individual gene promoters, and its efficacy is modulated by perturbations to chromatin modification machinery.
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Affiliation(s)
- Peter L Freddolino
- Department of Systems BiologyColumbia UniversityNew York CityUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew York CityUnited States
| | - Jamie Yang
- Department of Systems BiologyColumbia UniversityNew York CityUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew York CityUnited States
| | - Amir Momen-Roknabadi
- Department of Systems BiologyColumbia UniversityNew York CityUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew York CityUnited States
| | - Saeed Tavazoie
- Department of Systems BiologyColumbia UniversityNew York CityUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew York CityUnited States
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22
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Westphal LL, Lau J, Negro Z, Moreno IJ, Ismail Mohammed W, Lee H, Tang H, Finkel SE, Kram KE. Adaptation of Escherichia coli to long-term batch culture in various rich media. Res Microbiol 2018; 169:145-156. [PMID: 29454026 DOI: 10.1016/j.resmic.2018.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 12/22/2017] [Accepted: 01/23/2018] [Indexed: 12/29/2022]
Abstract
Experimental evolution studies have characterized the genetic strategies microbes utilize to adapt to their environments, mainly focusing on how microbes adapt to constant and/or defined environments. Using a system that incubates Escherichia coli in different complex media in long-term batch culture, we have focused on how heterogeneity and environment affects adaptive landscapes. In this system, there is no passaging of cells, and therefore genetic diversity is lost only through negative selection, without the experimentally-imposed bottlenecking common in other platforms. In contrast with other experimental evolution systems, because of cycling of nutrients and waste products, this is a heterogeneous environment, where selective pressures change over time, similar to natural environments. We determined that incubation in each environment leads to different adaptations by observing the growth advantage in stationary phase (GASP) phenotype. Re-sequencing whole genomes of populations identified both mutant alleles in a conserved set of genes and differences in evolutionary trajectories between environments. Reconstructing identified mutations in the parental strain background confirmed the adaptive advantage of some alleles, but also identified a surprising number of neutral or even deleterious mutations. This result indicates that complex epistatic interactions may be under positive selection within these heterogeneous environments.
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Affiliation(s)
- Lacey L Westphal
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, RRI 303, 1050 Child's Way, Los Angeles, CA, 90089-2910, USA.
| | - Jasmine Lau
- Department of Biology, California State University, Dominguez Hills, NSM A-137, 1000 E. Victoria Street, Carson, CA, 90747, USA.
| | - Zuly Negro
- Department of Biology, California State University, Dominguez Hills, NSM A-137, 1000 E. Victoria Street, Carson, CA, 90747, USA.
| | - Ivan J Moreno
- Department of Biology, California State University, Dominguez Hills, NSM A-137, 1000 E. Victoria Street, Carson, CA, 90747, USA.
| | - Wazim Ismail Mohammed
- School of Informatics and Computing, Indiana University, 150 S. Woodlawn Avenue, Bloomington, IN, 47405, USA.
| | - Heewook Lee
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, GHC 7719, 5000 Forbes Ave., Pittsburgh, PA, 15213, USA.
| | - Haixu Tang
- School of Informatics and Computing, Indiana University, 150 S. Woodlawn Avenue, Bloomington, IN, 47405, USA.
| | - Steven E Finkel
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, RRI 303, 1050 Child's Way, Los Angeles, CA, 90089-2910, USA.
| | - Karin E Kram
- Department of Biology, California State University, Dominguez Hills, NSM A-137, 1000 E. Victoria Street, Carson, CA, 90747, USA.
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23
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Shapiro JA. Living Organisms Author Their Read-Write Genomes in Evolution. BIOLOGY 2017; 6:E42. [PMID: 29211049 PMCID: PMC5745447 DOI: 10.3390/biology6040042] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/17/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022]
Abstract
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with "non-coding" DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called "non-coding" RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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24
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Reinterpreting Long-Term Evolution Experiments: Is Delayed Adaptation an Example of Historical Contingency or a Consequence of Intermittent Selection? J Bacteriol 2016; 198:1009-12. [PMID: 26883821 DOI: 10.1128/jb.00110-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Van Hofwegen et al. demonstrated that Escherichia coli rapidly evolves the ability to use citrate when long selective periods are provided (D. J. Van Hofwegen, C. J. Hovde, and S. A. Minnich, J Bacteriol 198:1022-1034, 2016, http://dx.doi.org/10.1128/JB.00831-15). This contrasts with the extreme delay (15 years of daily transfers) seen in the long-term evolution experiments of Lenski and coworkers. Their idea of "historical contingency" may require reinterpretation. Rapid evolution seems to involve selection for duplications of the whole cit locus that are too unstable to contribute when selection is provided in short pulses.
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