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Trends in Microbiology Jun 2020
Topics: Metabolic Engineering; Pseudomonas putida; Synthetic Biology
PubMed: 32396829
DOI: 10.1016/j.tim.2020.02.015 -
Journal of Biotechnology Jun 2023Mevalonate, an important intermediate product of the mevalonate pathway, has a broad spectrum of applications. With the rapid growth of metabolic engineering and... (Review)
Review
Mevalonate, an important intermediate product of the mevalonate pathway, has a broad spectrum of applications. With the rapid growth of metabolic engineering and synthetic biology, mevalonate biosynthesis by microorganisms is feasible and holds great promise in the future. In this review, we summarize the applications of mevalonate and its derivatives and describe the biosynthesis pathways of mevalonate. The current status of mevalonate biosynthesis is also detailed with an emphasis on metabolic engineering strategies to enhance mevalonate production in typical industrial organisms, including Escherichia coli, Saccharomyces cerevisiae, and Pseudomonas putida, suggesting new insights for the efficient production of biosynthesized mevalonate.
Topics: Mevalonic Acid; Escherichia coli; Metabolic Engineering; Saccharomyces cerevisiae; Pseudomonas putida
PubMed: 37209831
DOI: 10.1016/j.jbiotec.2023.05.005 -
Applied Microbiology and Biotechnology May 2022Plant growth-promoting rhizobacteria (PGPR) are a group of microorganisms of utmost interest in agricultural biotechnology for their stimulatory and protective effects... (Review)
Review
Plant growth-promoting rhizobacteria (PGPR) are a group of microorganisms of utmost interest in agricultural biotechnology for their stimulatory and protective effects on plants. Among the various PGPR species, some Pseudomonas putida strains combine outstanding traits such as phytohormone synthesis, nutrient solubilization, adaptation to different stress conditions, and excellent root colonization ability. In this review, we summarize the state of the art and the most relevant findings related to P. putida and its close relatives as PGPR, and we have compiled a detailed list of P. putida sensu stricto, sensu lato, and close relative strains that have been studied for their plant growth-promoting characteristics. However, the mere in vitro analysis of these characteristics does not guarantee correct plant performance under in vivo or field conditions. Therefore, the importance of studying adhesion and survival in the rhizosphere, as well as responses to environmental factors, is emphasized. Although numerous strains of this species have shown good performance in field trials, their use in commercial products is still very limited. Thus, we also analyze the opportunities and challenges related to the formulation and application of bioproducts based on these bacteria. KEY POINTS: •The mini-review updates the knowledge on Pseudomonas putida as a PGPR. • Some rhizosphere strains are able to improve plant growth under stress conditions. • The metabolic versatility of this species encourages the development of a bioproduct.
Topics: Plant Development; Plant Growth Regulators; Plant Roots; Plants; Pseudomonas putida; Rhizosphere; Soil Microbiology
PubMed: 35488932
DOI: 10.1007/s00253-022-11881-7 -
Applied Microbiology and Biotechnology Sep 2020Pseudomonas putida is a Gram-negative, rod-shaped bacterium that can be encountered in diverse ecological habitats. This ubiquity is traced to its remarkably versatile... (Review)
Review
Pseudomonas putida is a Gram-negative, rod-shaped bacterium that can be encountered in diverse ecological habitats. This ubiquity is traced to its remarkably versatile metabolism, adapted to withstand physicochemical stress, and the capacity to thrive in harsh environments. Owing to these characteristics, there is a growing interest in this microbe for industrial use, and the corresponding research has made rapid progress in recent years. Hereby, strong drivers are the exploitation of cheap renewable feedstocks and waste streams to produce value-added chemicals and the steady progress in genetic strain engineering and systems biology understanding of this bacterium. Here, we summarize the recent advances and prospects in genetic engineering, systems and synthetic biology, and applications of P. putida as a cell factory. KEY POINTS: • Pseudomonas putida advances to a global industrial cell factory. • Novel tools enable system-wide understanding and streamlined genomic engineering. • Applications of P. putida range from bioeconomy chemicals to biosynthetic drugs.
Topics: Biotechnology; Genomics; Pseudomonas putida; Synthetic Biology; Systems Biology
PubMed: 32789744
DOI: 10.1007/s00253-020-10811-9 -
Journal of Medical Microbiology Mar 2020is a fast-growing bacterium found mostly in temperate soil and water habitats. The metabolic versatility of makes this organism attractive for biotechnological... (Review)
Review
is a fast-growing bacterium found mostly in temperate soil and water habitats. The metabolic versatility of makes this organism attractive for biotechnological applications such as biodegradation of environmental pollutants and synthesis of added-value chemicals (biocatalysis). This organism has been extensively studied in respect to various stress responses, mechanisms of genetic plasticity and transcriptional regulation of catabolic genes. is able to colonize the surface of living organisms, but is generally considered to be of low virulence. A number of strains are able to promote plant growth. The aim of this review is to give historical overview of the discovery of the species and isolation and characterization of strains displaying potential for biotechnological applications. This review also discusses some major findings in research encompassing regulation of catabolic operons, stress-tolerance mechanisms and mechanisms affecting evolvability of bacteria under conditions of environmental stress.
Topics: Biodegradation, Environmental; Biological Evolution; Biotechnology; Host-Pathogen Interactions; Humans; Metabolism; Operon; Pseudomonas Infections; Pseudomonas putida; Stress, Physiological
PubMed: 31958045
DOI: 10.1099/jmm.0.001137 -
Biotechnology Journal Mar 2021Growing environmental concern sparks renewed interest in the sustainable production of (bio)materials that can replace oil-derived goods. Polyhydroxyalkanoates (PHAs)... (Review)
Review
Growing environmental concern sparks renewed interest in the sustainable production of (bio)materials that can replace oil-derived goods. Polyhydroxyalkanoates (PHAs) are isotactic polymers that play a critical role in the central metabolism of producer bacteria, as they act as dynamic reservoirs of carbon and reducing equivalents. PHAs continue to attract industrial attention as a starting point toward renewable, biodegradable, biocompatible, and versatile thermoplastic and elastomeric materials. Pseudomonas species have been known for long as efficient biopolymer producers, especially for medium-chain-length PHAs. The surge of synthetic biology and metabolic engineering approaches in recent years offers the possibility of exploiting the untapped potential of Pseudomonas cell factories for the production of tailored PHAs. In this article, an overview of the metabolic and regulatory circuits that rule PHA accumulation in Pseudomonas putida is provided, and approaches leading to the biosynthesis of novel polymers (e.g., PHAs including nonbiological chemical elements in their structures) are discussed. The potential of novel PHAs to disrupt existing and future market segments is closer to realization than ever before. The review is concluded by pinpointing challenges that currently hinder the wide adoption of bio-based PHAs, and strategies toward programmable polymer biosynthesis from alternative substrates in engineered P. putida strains are proposed.
Topics: Carbon; Metabolic Engineering; Polyhydroxyalkanoates; Pseudomonas; Pseudomonas putida
PubMed: 33085217
DOI: 10.1002/biot.202000165 -
Environmental Microbiology Sep 2023Pseudomonads are considered to be among the most widespread culturable bacteria in mesophilic environments. The evolutive success of Pseudomonas species can be... (Review)
Review
Pseudomonads are considered to be among the most widespread culturable bacteria in mesophilic environments. The evolutive success of Pseudomonas species can be attributed to their metabolic versatility, in combination with a set of additional functions that enhance their ability to colonize different niches. These include the production of secondary metabolites involved in iron acquisition or having a detrimental effect on potential competitors, different types of motility, and the capacity to establish and persist within biofilms. Although biofilm formation has been extensively studied using the opportunistic pathogen Pseudomonas aeruginosa as a model organism, a significant body of knowledge is also becoming available for non-pathogenic Pseudomonas. In this review, we focus on the mechanisms that allow Pseudomonas putida to colonize biotic and abiotic surfaces and adapt to sessile life, as a relevant persistence strategy in the environment. This species is of particular interest because it includes plant-beneficial strains, in which colonization of plant surfaces may be relevant, and strains used for environmental and biotechnological applications, where the design and functionality of biofilm-based bioreactors, for example, also have to take into account the efficiency of bacterial colonization of solid surfaces. This work reviews the current knowledge of mechanistic and regulatory aspects of biofilm formation by P. putida and pinpoints the prospects in this field.
Topics: Pseudomonas putida; Pseudomonas; Biofilms; Pseudomonas aeruginosa; Plants
PubMed: 37045787
DOI: 10.1111/1462-2920.16385 -
Environmental Microbiology Jan 2022A single region of the Pseudomonas putida genome, designated the flagellar cluster, includes 59 genes potentially involved in the biogenesis and function of the...
A single region of the Pseudomonas putida genome, designated the flagellar cluster, includes 59 genes potentially involved in the biogenesis and function of the flagellar system. Here, we combine bioinformatics and in vivo gene expression analyses to clarify the transcriptional organization and regulation of the flagellar genes in the cluster. We have identified 11 flagellar operons and characterized 22 primary and internal promoter regions. Our results indicate that synthesis of the flagellar apparatus and core chemotaxis machinery is regulated by a three-tier cascade in which fleQ is a Class I gene, standing at the top of the transcriptional hierarchy. FleQ- and σ -dependent Class II genes encode most components of the flagellar structure, part of the chemotaxis machinery and multiple regulatory elements, including the flagellar σ factor FliA. FliA activation of Class III genes enables synthesis of the filament, one stator complex and completion of the chemotaxis apparatus. Accessory regulatory proteins and an intricate operon architecture add complexity to the regulation by providing feedback and feed-forward loops to the main circuit. Because of the high conservation of the gene arrangement and promoter motifs, we believe that the regulatory circuit presented here may also apply to other environmental pseudomonads.
Topics: Bacterial Proteins; Flagella; Gene Expression Regulation, Bacterial; Pseudomonas putida; Sigma Factor; Transcription, Genetic
PubMed: 34859548
DOI: 10.1111/1462-2920.15857 -
ACS Synthetic Biology Nov 2022KT2440 is an emerging microbial chassis for biobased chemical production from renewable feedstocks and environmental bioremediation. However, tools for studying,...
KT2440 is an emerging microbial chassis for biobased chemical production from renewable feedstocks and environmental bioremediation. However, tools for studying, engineering, and modulating protein complexes and biosynthetic enzymes in this organism are largely underdeveloped. Genetic code expansion for the incorporation of unnatural amino acids (unAAs) into proteins can advance such efforts and, furthermore, enable additional controls of biological processes of the strain. In this work, we established the orthogonality of two widely used archaeal tRNA synthetase and tRNA pairs in KT2440. Following the optimization of decoding systems, four unAAs were incorporated into proteins in response to a UAG stop codon at 34.6-78% efficiency. In addition, we demonstrated the utility of genetic code expansion through the incorporation of a photocross-linking amino acid, -benzoyl-l-phenylalanine (pBpa), into glutathione -transferase (GstA) and a chemosensory response regulator (CheY) for protein-protein interaction studies in KT2440. This work reported the successful genetic code expansion in KT2440 for the first time. Given the diverse structure and functions of unAAs that have been added to protein syntheses using the archaeal systems, our research lays down a solid foundation for future work to study and enhance the biological functions of KT2440.
Topics: Pseudomonas putida; Genetic Code; Amino Acyl-tRNA Synthetases; RNA, Transfer; Amino Acids
PubMed: 36287825
DOI: 10.1021/acssynbio.2c00325 -
Microbes and Environments 2023Pseudomonas putida is a major species belonging to the genus Pseudomonas. Although several hundred strains of P. putida have been deposited in culture collections, they...
Pseudomonas putida is a major species belonging to the genus Pseudomonas. Although several hundred strains of P. putida have been deposited in culture collections, they potentially differ from the genetically defined "true Pseudomonas putida" because many were classified as P. putida based on their phenotypic and metabolic characteristics. A phylogenetic ana-lysis based on the concatenated sequences of the 16S rRNA and rpoD genes revealed that 46 strains of P. putida deposited in Japanese culture collections were classified into nine operational taxonomic units (OTUs) and eleven singletons. The OTU7 strain produces N-acylhomoserine lactone as a quorum-sensing signal. One of the OTU7 strains, JCM 20066, exhibited a ppuI-rsaL-ppuR quorum-sensing system that controls biofilm formation and motility. The P. putida type strain JCM 13063 and six other strains were classified as OTU4. Classification based on the calculation of whole-genome similarity revealed that three OTU4 strains, JCM 20005, 21368, and 13061, were regarded as the same species as JCM 13063 and defined as true P. putida. When orthologous genes in the whole-genome sequences of true P. putida strains were screened, PP4_28660 from P. putida NBRC 14164 (=JCM 13063) was present in all true P. putida genome sequences. The internal region of PP4_28660 was successfully amplified from all true P. putida strains using the specific primers designed in this study.
Topics: Bacterial Typing Techniques; DNA, Bacterial; Fatty Acids; Genomics; Phylogeny; Pseudomonas putida; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 37286511
DOI: 10.1264/jsme2.ME23019