Review

Authors: Mitchell Andrews, Morag E Andrews

Most species in the Leguminosae (legume family) can fix atmospheric nitrogen (N₂) via symbiotic bacteria (rhizobia) in root nodules. Here, the literature on legume-rhizobia symbioses in field soils was reviewed and genotypically characterised rhizobia related to the taxonomy of the legumes from which they were isolated. The Leguminosae was divided into three sub-families, the Caesalpinioideae, Mimosoideae and Papilionoideae. spp. were the exclusive rhizobial symbionts of species in the Caesalpinioideae, but data are limited. Generally, a range of rhizobia genera nodulated legume species across the two Mimosoideae tribes Ingeae and Mimoseae, but spp. show specificity towards in central and southern Brazil, / in central Mexico and in southern Uruguay. These specific symbioses are likely to be at least in part related to the relative occurrence of the potential symbionts in soils of the different regions. Generally, Papilionoideae species were promiscuous in relation to rhizobial symbionts, but specificity for rhizobial genus appears to hold at the tribe level for the Fabeae (), the genus level for (), () and the New Zealand native spp. () and species level for (), () and (). Specificity for rhizobial species/symbiovar appears to hold for ( sv. ) ( sv. ), (), ( sv. ), ( sv. s) and ( sv. ). Lateral gene transfer of specific symbiosis genes within rhizobial genera is an important mechanism allowing legumes to form symbioses with rhizobia adapted to particular soils. Strain-specific legume rhizobia symbioses can develop in particular habitats.

Topics: Bacterial Proteins; Bradyrhizobium; Cupriavidus; Fabaceae; Phylogeny; Plant Roots; RNA, Ribosomal, 16S; Rhizobium; Symbiosis

PubMed: 28346361
DOI: 10.3390/ijms18040705

Review

Authors: Anna Jarosławiecka, Zofia Piotrowska-Seget

Lead (Pb) is an element present in the environment that negatively affects all living organisms. To diminish its high toxicity, micro-organisms have developed several mechanisms that allow them to survive exposure to Pb(II). The main mechanisms of lead resistance involve adsorption by extracellular polysaccharides, cell exclusion, sequestration as insoluble phosphates, and ion efflux to the cell exterior. This review describes the various lead resistance mechanisms, and the regulation of their expression by lead binding regulatory proteins. Special attention is given to the Pbr system from Cupriavidus metallidurans CH34, which involves a unique mechanism combining efflux and lead precipitation.

Topics: Cupriavidus; Drug Resistance, Bacterial; Lead; Metabolic Networks and Pathways

PubMed: 24124204
DOI: 10.1099/mic.0.070284-0

Review

Authors: Milton H Saier, Chika Kukita, Zhongge Zhang...

Transposon-mediated "directed" mutations occur at higher frequencies when beneficial than when detrimental and relieve the stress that causes them. The first and best-studied example involves regulation of Insertion Sequence-5 (IS5) insertion into a specific activating site upstream of the glycerol utilization operon in , . This event promotes high level expression of the operon, allowing glycerol utilization in wild type cells under inhibitory conditions. The phosphoenolpyruvate-dependent, sugar transporting, phosphotransferase system (PTS) influences this process by regulating cytoplasmic glycerol-3-phosphate and cyclic AMP concentrations. Insertion frequencies are determined by IS5-specific tetranucleotide target sequences in stress-induced (DNA) duplex destabilization (SIDD) structures counteracted by two DNA binding proteins, GlpR and Crp which directly inhibit insertion, responding to cytoplasmic glycerol-3-phosphate and cyclic AMP, respectively. Expression of the master regulator of flagellar gene control, , is subject to activation by IS elements by a directed mechanism, and zinc-induced transposon-mediated zinc resistance has been demonstrated in . The use of DNA conformation and DNA binding proteins to control transposon hopping also occurs in eukaryotes.

Topics: Bacteria; Cupriavidus; DNA Transposable Elements; Escherichia coli; Eukaryota; Evolution, Molecular; Mutation; Operon; Phosphoenolpyruvate Sugar Phosphotransferase System; Zinc

PubMed: 28199212
DOI: 10.2741/4553

Authors: Ernesta Augustiniene, Naglis Malys

Lactic acid is an important platform chemical used for the production of various compounds including polylactic acid (PLA). Optically pure L- and D-lactic acids are required to obtain high quality PLA. To advance the development and selection of microbial strains for improved production of lactic acid enantiomers, a high-throughput screening, dynamic pathway control, or real-time monitoring are often applied. Inducible gene expression systems and their application in the genetically encoded biosensors contribute to the development of these techniques and are important devices for the advancement of lactic acid biotechnology. Here, we identify and characterize eleven lactate-inducible systems from Escherichia coli, Cupriavidus necator, and Pseudomonas spp. The specificity and dynamics of these systems in response to L- and D-lactate, or structurally similar compounds are investigated. We demonstrate that the inducible systems EcLldR/P and CnGntR/P respond only to the L-lactate, exhibiting approximately 19- and 24-fold induction, respectively. Despite neither of the examined bacteria possess the D-lactate-specific inducible system, the PaPdhR/P and PfPdhR/P are induced approximately 37- and 366-fold, respectively, by D-lactate and can be used for developing biosensor with improved specificity. The findings of this study provide an insight into understanding of L- and D-lactate-inducible systems that can be employed as sensing and tuneable devices in synthetic biology.

Topics: Biosensing Techniques; Cupriavidus necator; Escherichia coli; Lactic Acid; Multigene Family; Pseudomonas; Synthetic Biology

PubMed: 35136142
DOI: 10.1038/s41598-022-06028-7

Authors: Niklas Hirth, Michelle-Sophie Gerlach, Nicole Wiesemann...

The metal-resistant bacterium Cupriavidus metallidurans uses its copper resistance components to survive the synergistic toxicity of copper ions and gold complexes in auriferous soils. The , , , and determinants encode as central component the Cu(I)-exporting P-type ATPase CupA, the periplasmic Cu(I)-oxidase CopA, the transenvelope efflux system CusCBA, and the Gig system with unknown function, respectively. The interplay of these systems with each other and with glutathione (GSH) was analyzed. Copper resistance in single and multiple mutants up to the quintuple mutant was characterized in dose-response curves, Live/Dead-staining, and atomic copper and glutathione content of the cells. The regulation of the and determinants was studied using reporter gene fusions and in case of also RT-PCR studies, which verified the operon structure of . All five systems contributed to copper resistance in the order of importance: Cup, Cop, Cus, GSH, and Gig. Only Cup was able to increase copper resistance of the Δ quintuple mutant but the other systems were required to increase copper resistance of the Δ quadruple mutant to the parent level. Removal of the Cop system resulted in a clear decrease of copper resistance in most strain backgrounds. Cus cooperated with and partially substituted Cop. Gig and GSH cooperated with Cop, Cus, and Cup. Copper resistance is thus the result of an interplay of many systems. The ability of bacteria to maintain homeostasis of the essential-but-toxic "Janus"-faced element copper is important for their survival in many natural environments but also in case of pathogenic bacteria in their respective host. The most important contributors to copper homeostasis have been identified in the last decades and comprise P-type ATPases, periplasmic copper- and oxygen-dependent copper oxidases, transenvelope efflux systems, and glutathione; however, it is not known how all these players interact. This publication investigates this interplay and describes copper homeostasis as a trait emerging from a network of interacting resistance systems.

Topics: Bacterial Proteins; Cupriavidus; Gold; Genes, Reporter

PubMed: 37191542
DOI: 10.1128/aem.00567-23

Review

Authors: Maria Silvia Morlino, Rebecca Serna García, Filippo Savio...

Cupriavidus necator is a bacterium with a high phenotypic diversity and versatile metabolic capabilities. It has been extensively studied as a model hydrogen oxidizer, as well as a producer of polyhydroxyalkanoates (PHA), plastic-like biopolymers with a high potential to substitute petroleum-based materials. Thanks to its adaptability to diverse metabolic lifestyles and to the ability to accumulate large amounts of PHA, C. necator is employed in many biotechnological processes, with particular focus on PHA production from waste carbon sources. The large availability of genomic information has enabled a characterization of C. necator's metabolism, leading to the establishment of metabolic models which are used to devise and optimize culture conditions and genetic engineering approaches. In this work, the characteristics of available C. necator strains and genomes are reviewed, underlining how a thorough comprehension of the genetic variability of C. necator is lacking and it could be instrumental for wider application of this microorganism. The metabolic paradigms of C. necator and how they are connected to PHA production and accumulation are described, also recapitulating the variety of carbon substrates used for PHA accumulation, highlighting the most promising strategies to increase the yield. Finally, the review describes and critically analyzes currently available genome-scale metabolic models and reduced metabolic network applications commonly employed in the optimization of PHA production. Overall, it appears that the capacity of C. necator of performing CO bioconversion to PHA is still underexplored, both in biotechnological applications and in metabolic modeling. However, the accurate characterization of this organism and the efforts in using it for gas fermentation can help tackle this challenging perspective in the future.

Topics: Polyhydroxyalkanoates; Cupriavidus necator; Fermentation; Biotechnology; Carbon

PubMed: 37775073
DOI: 10.1016/j.biotechadv.2023.108264

Review

Authors: Hanna Rosigkeit, Lea Kneißle, Stanislav Obruča...

An astonishing variety of functions has been attributed to polyphosphate (polyP) in prokaryotes. Besides being a reservoir of phosphorus, functions in exopolysaccharide formation, motility, virulence and in surviving various forms of stresses such as exposure to heat, extreme pH, oxidative agents, high osmolarity, heavy metals and others have been ascribed to polyP. In this contribution, we will provide a historical overview on polyP, will then describe the key proteins of polyP synthesis, the polyP kinases, before we will critically assess of the underlying data on the multiple functions of polyP and provide evidence that - with the exception of a P-storage-function - most other functions of polyP are not relevant for survival of Ralstonia eutropha, a biotechnologically important beta-proteobacterial species.

Topics: Cupriavidus necator; Polyphosphates

PubMed: 34015783
DOI: 10.1159/000515741

Review

Authors: Justin Panich, Bonnie Fong, Steven W Singer...

Decelerating global warming is one of the predominant challenges of our time and will require conversion of CO to usable products and commodity chemicals. Of particular interest is the production of fuels, because the transportation sector is a major source of CO emissions. Here, we review recent technological advances in metabolic engineering of the hydrogen-oxidizing bacterium Cupriavidus necator H16, a chemolithotroph that naturally consumes CO to generate biomass. We discuss recent successes in biofuel production using this organism, and the implementation of electrolysis/artificial photosynthesis approaches that enable growth of C. necator using renewable electricity and CO. Last, we discuss prospects of improving the nonoptimal growth of C. necator in ambient concentrations of CO.

Topics: Biofuels; Carbon Dioxide; Cupriavidus necator; Hydrogen; Metabolic Engineering

PubMed: 33518389
DOI: 10.1016/j.tibtech.2021.01.001

Authors: Catherine Fan, Paul A Davison, Robert Habgood...

A type of chromosome-free cell called SimCells (simple cells) has been generated from , , and The removal of the native chromosomes of these bacteria was achieved by double-stranded breaks made by heterologous I-CeuI endonuclease and the degradation activity of endogenous nucleases. We have shown that the cellular machinery remained functional in these chromosome-free SimCells and was able to process various genetic circuits. This includes the glycolysis pathway (composed of 10 genes) and inducible genetic circuits. It was found that the glycolysis pathway significantly extended longevity of SimCells due to its ability to regenerate ATP and NADH/NADPH. The SimCells were able to continuously express synthetic genetic circuits for 10 d after chromosome removal. As a proof of principle, we demonstrated that SimCells can be used as a safe agent (as they cannot replicate) for bacterial therapy. SimCells were used to synthesize catechol (a potent anticancer drug) from salicylic acid to inhibit lung, brain, and soft-tissue cancer cells. SimCells represent a simplified synthetic biology chassis that can be programmed to manufacture and deliver products safely without interference from the host genome.

Topics: Antineoplastic Agents; Catechols; Cell Proliferation; Cellular Reprogramming; Chromosomes, Bacterial; Cupriavidus necator; Drug Delivery Systems; Escherichia coli; Gene Regulatory Networks; Genetic Engineering; Neoplasms; Pseudomonas putida; Synthetic Biology; Tumor Cells, Cultured

PubMed: 32144140
DOI: 10.1073/pnas.1918859117

Authors: Michelle-Sophie Gerlach, Peter Neubauer, Matthias Gimpel...

OBJECTIVES

Research on hydrogenases from Cupriavidus necator has been ongoing for more than two decades and still today the common methods for culture inoculation are used. These methods were never adapted to the requirements of modified bacterial strains, resulting in different physiological states of the bacteria in the precultures, which in turn lead prolonged and different lag-phases.

RESULTS

In order to obtain uniform and always equally fit precultures for inoculation, we have established in this study an optimized protocol for precultures of the derivative of C. necator HF210 (C. necator HP80) which is used for homologous overexpression of the genes for the NAD-reducing soluble hydrogenase (SH). We compared different media for preculture growth and determined the optimal time point for harvest. The protocol obtained in this study is based on two subsequent precultures, the first one in complex nutrient broth medium (NB) and a second one in fructose -nitrogen mineral salt medium (FN).

CONCLUSION

Despite having two subsequent precultures our protocol reduces the preculture time to less than 30 h and provides reproducible precultures for cultivation of C. necator HP80.

Topics: Cupriavidus necator; Hydrogenase; Culture Media; Nitrogen; Fructose

PubMed: 37828291
DOI: 10.1007/s10529-023-03436-1