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Biotechnology Advances Nov 2022Rhodopseudomonas palustris is an attractive option for biotechnical applications and industrial engineering due to its metabolic versatility and its ability to... (Review)
Review
Rhodopseudomonas palustris is an attractive option for biotechnical applications and industrial engineering due to its metabolic versatility and its ability to catabolize a wide variety of feedstocks and convert them to several high-value products. Given its adaptable metabolism, R. palustris has been studied and applied in an extensive variety of applications such as examining metabolic tradeoffs for environmental perturbations, biodegradation of aromatic compounds, environmental remediation, biofuel production, agricultural biostimulation, and bioelectricity production. This review provides a holistic summary of the commercial applications for R. palustris as a biotechnology chassis and suggests future perspectives for research and engineering.
Topics: Biodegradation, Environmental; Biofuels; Biotechnology; Rhodopseudomonas
PubMed: 35680002
DOI: 10.1016/j.biotechadv.2022.108001 -
Communications Biology Nov 2021Anthropogenic carbon dioxide (CO) release in the atmosphere from fossil fuel combustion has inspired scientists to study CO to biofuel conversion. Oxygenic phototrophs...
Anthropogenic carbon dioxide (CO) release in the atmosphere from fossil fuel combustion has inspired scientists to study CO to biofuel conversion. Oxygenic phototrophs such as cyanobacteria have been used to produce biofuels using CO. However, oxygen generation during oxygenic photosynthesis adversely affects biofuel production efficiency. To produce n-butanol (biofuel) from CO, here we introduce an n-butanol biosynthesis pathway into an anoxygenic (non-oxygen evolving) photoautotroph, Rhodopseudomonas palustris TIE-1 (TIE-1). Using different carbon, nitrogen, and electron sources, we achieve n-butanol production in wild-type TIE-1 and mutants lacking electron-consuming (nitrogen-fixing) or acetyl-CoA-consuming (polyhydroxybutyrate and glycogen synthesis) pathways. The mutant lacking the nitrogen-fixing pathway produce the highest n-butanol. Coupled with novel hybrid bioelectrochemical platforms, this mutant produces n-butanol using CO, solar panel-generated electricity, and light with high electrical energy conversion efficiency. Overall, this approach showcases TIE-1 as an attractive microbial chassis for carbon-neutral n-butanol bioproduction using sustainable, renewable, and abundant resources.
Topics: 1-Butanol; Biosynthetic Pathways; Carbon; Electrons; Nitrogen; Rhodopseudomonas
PubMed: 34732832
DOI: 10.1038/s42003-021-02781-z -
Proceedings of the National Academy of... Jun 2022Solar-driven bioelectrosynthesis represents a promising approach for converting abundant resources into value-added chemicals with renewable energy. Microorganisms...
Solar-driven bioelectrosynthesis represents a promising approach for converting abundant resources into value-added chemicals with renewable energy. Microorganisms powered by electrochemical reducing equivalents assimilate CO, HO, and N building blocks. However, products from autotrophic whole-cell biocatalysts are limited. Furthermore, biocatalysts tasked with N reduction are constrained by simultaneous energy-intensive autotrophy. To overcome these challenges, we designed a biohybrid coculture for tandem and tunable CO and N fixation to value-added products, allowing the different species to distribute bioconversion steps and reduce the individual metabolic burden. This consortium involves acetogen , which reduces CO to acetate, and diazotrophic , which uses the acetate both to fuel N fixation and for the generation of a biopolyester. We demonstrate that the coculture platform provides a robust ecosystem for continuous CO and N fixation, and its outputs are directed by substrate gas composition. Moreover, we show the ability to support the coculture on a high-surface area silicon nanowire cathodic platform. The biohybrid coculture achieved peak faradaic efficiencies of 100, 19.1, and 6.3% for acetate, nitrogen in biomass, and ammonia, respectively, while maintaining product tunability. Finally, we established full solar to chemical conversion driven by a photovoltaic device, resulting in solar to chemical efficiencies of 1.78, 0.51, and 0.08% for acetate, nitrogenous biomass, and ammonia, correspondingly. Ultimately, our work demonstrates the ability to employ and electrochemically manipulate bacterial communities on demand to expand the suite of CO and N bioelectrosynthesis products.
Topics: Acetates; Ammonia; Carbon Dioxide; Coculture Techniques; Ecosystem; Firmicutes; Nitrogen; Nitrogen Fixation; Photosynthesis; Rhodopseudomonas
PubMed: 35727971
DOI: 10.1073/pnas.2122364119 -
MBio Apr 2023How bacteria transition into growth arrest as part of stationary phase has been well-studied, but our knowledge of features that help cells to stay alive in the...
How bacteria transition into growth arrest as part of stationary phase has been well-studied, but our knowledge of features that help cells to stay alive in the following days and weeks is incomplete. Most studies have used heterotrophic bacteria that are growth-arrested by depletion of substrates used for both biosynthesis and energy generation, making is difficult to disentangle the effects of the two. In contrast, when grown anaerobically in light, the phototrophic bacterium Rhodopseudomonas palustris generates ATP from light via cyclic photophosphorylation, and builds biomolecules from organic substrates, such as acetate. As such, energy generation and carbon utilization are independent from one another. Here, we compared the physiological and molecular responses of R. palustris to growth arrest caused by carbon source depletion in light (energy-replete) and dark (energy-depleted) conditions. Both sets of cells remained viable for 6 to 10 days, at which point dark-incubated cells lost viability, whereas light-incubated cells remained fully viable for 60 days. Dark-incubated cells were depleted in intracellular ATP prior to losing viability, suggesting that ATP depletion is a cause of cell death. Dark-incubated cells also shut down measurable protein synthesis, whereas light-incubated cells continued to synthesize proteins at low levels. Cells incubated in both conditions continued to transcribe genes. We suggest that R. palustris may completely shut down protein synthesis in dark, energy-depleted, conditions as a strategy to survive the nighttime hours of day/night cycles it experiences in nature, where there is a predictable source of energy in the form of sunlight only during the day. The molecular and physiological basis of bacterial longevity in growth arrest is important to investigate for several reasons. Such investigations could improve treatment of chronic infections, advance use of non-growing bacteria as biocatalysts to make high yields of value-added products, and improve estimates of microbial activities in natural habitats, where cells are often growing slowly or not at all. Here, we compared survival of the phototrophic bacterium Rhodopseudomonas palustris under conditions where it generates ATP (incubation in light), and where it does not generate ATP (incubation in dark) to directly assess effects of energy depletion on long-term viability. We found that ATP is important for long-term survival over weeks. However, R. palustris survives 12 h periods of ATP depletion without loss of viability, apparently in anticipation of sunrise and restoration of its ability to generate ATP. Our work suggests that cells respond to ATP depletion by shutting down protein synthesis.
Topics: Longevity; Rhodopseudomonas; Carbon; Adenosine Triphosphate
PubMed: 36786592
DOI: 10.1128/mbio.03609-22 -
MicrobiologyOpen Dec 2019An approach to culturing attached and suspended forms of Rhodopseudomonas faecalis by using compound fish feed with tap water in transparent containers is reported in...
An approach to culturing attached and suspended forms of Rhodopseudomonas faecalis by using compound fish feed with tap water in transparent containers is reported in this study. The ratio of fish feed to tap water was 14.3-50.8 g/L, and no other inoculum or substances were added during the culture process. When the ratio of fish feed to tap water was 14.3 g/L, the highest total nitrogen, total phosphorus, and total dissolved carbon content recorded in the water in the containers were approximately 730 mg/L, 356 mg/L, and 1,620 mg/L, respectively, during the process of feed decay. Comamonas, Rhodopseudomonas, and Clostridium successively dominated during the culture process. Rhodopseudomonas was the most common dominant genus in both the attached and suspended forms when the water was dark red, and the relative operational taxonomic unit abundance reached 80-89% and 24.8%, respectively. The dominant species was R. faecalis. The maximum thickness of attached bacteria and the biomass of attached Rhodopseudomonas reached up to 0.56 mm and 7.5 mg/cm , respectively. This study provides a method for the mass culture of Rhodopseudomonas by using the fermentation of aquatic compound fish feed.
Topics: Animal Feed; Animals; Biomass; Fermentation; Fishes; Metagenome; Metagenomics; Microbiota; Photosynthesis; Rhodopseudomonas; Water Microbiology
PubMed: 31482697
DOI: 10.1002/mbo3.924 -
BioMed Research International 2017Arsenic (As) is a well-known toxic metalloid found naturally and released by different industries, especially in developing countries. Purple nonsulfur bacteria (PNSB)...
Arsenic (As) is a well-known toxic metalloid found naturally and released by different industries, especially in developing countries. Purple nonsulfur bacteria (PNSB) are known for wastewater treatment and plant growth promoting abilities. As-resistant PNSB were isolated from a fish pond. Based on As-resistance and plant growth promoting attributes, 2 isolates CS2 and SS5 were selected and identified as and , respectively, through 16S rRNA gene sequencing. Maximum As(V) resistance shown by SS5 and CS2 was up to 150 and 100 mM, respectively. . CS2 showed highest As(V) reduction up to 62.9% (6.29 ± 0.24 mM), while SS5 showed maximum As(III) oxidation up to 96% (4.8 ± 0.32 mM), respectively. Highest auxin production was observed by CS2 and SS, up to 77.18 ± 3.7 and 76.67 ± 2.8 g mL, respectively. Effects of these PNSB were tested on the growth of plants. A statistically significant increase in growth was observed in plants inoculated with isolates compared to uninoculated plants, both in presence and in absence of As. CS2 treated plants showed 17% (28.1 ± 0.87 cm) increase in shoot length and 21.7% (7.07 ± 0.42 cm) increase in root length, whereas SS5 treated plants showed 12.8% (27.09 ± 0.81 cm) increase in shoot length and 18.8% (6.9 ± 0.34 cm) increase in root length as compared to the control plants. In presence of As, CS2 increased shoot length up to 26.3% (21.0 ± 1.1 cm), while root length increased up to 31.3% (5.3 ± 0.4 cm), whereas SS5 inoculated plants showed 25% (20.7 ± 1.4 cm) increase in shoot length and 33.3% (5.4 ± 0.65 cm) increase in root length as compared to the control plants. Bacteria with such diverse abilities could be ideal for plant growth promotion in As-contaminated sites.
Topics: Arsenic; Indoleacetic Acids; Oxidation-Reduction; Plant Development; RNA, Ribosomal, 16S; Rhodopseudomonas; Rhodospirillaceae; Vigna; Wastewater
PubMed: 28386559
DOI: 10.1155/2017/6250327 -
MBio Nov 2017It is well known that many bacteria can survive in a growth-arrested state for long periods of time, on the order of months or even years, without forming dormant...
It is well known that many bacteria can survive in a growth-arrested state for long periods of time, on the order of months or even years, without forming dormant structures like spores or cysts. How is such longevity possible? What is the molecular basis of such longevity? Here we used the Gram-negative phototrophic alphaproteobacterium to identify molecular determinants of bacterial longevity. maintained viability for over a month after growth arrest due to nutrient depletion when it was provided with light as a source of energy. In transposon sequencing (Tn-seq) experiments, we identified 117 genes that were required for long-term viability of nongrowing cells. Genes in this longevity gene set are annotated to play roles in a number of cellular processes, including DNA repair, tRNA modification, and the fidelity of protein synthesis. These genes are critically important only when cells are not growing. Three genes annotated to affect translation or posttranslational modifications were validated as longevity genes by mutagenesis and complementation experiments. These genes and others in the longevity gene set are broadly conserved in bacteria. This raises the possibility that it will be possible to define a core set of longevity genes common to many bacterial species. Bacteria in nature and during infections often exist in a nongrowing quiescent state. However, it has been difficult to define experimentally the molecular characteristics of this crucial element of the bacterial life cycle because bacteria that are not growing tend to die under laboratory conditions. Here we present and validate the phototrophic bacterium as a model system for identification of genes required for the longevity of nongrowing bacteria. Growth-arrested maintained almost full viability for weeks using light as an energy source. Such cells were subjected to large-scale mutagenesis to identify genes required for this striking longevity trait. The results define conserved determinants of survival under nongrowing conditions and create a foundation for more extensive studies to elucidate general molecular mechanisms of bacterial longevity.
Topics: DNA Transposable Elements; Genes, Bacterial; Microbial Viability; Molecular Sequence Annotation; Mutagenesis, Insertional; Rhodopseudomonas; Sequence Analysis, DNA
PubMed: 29184015
DOI: 10.1128/mBio.01726-17 -
Annual Review of Biochemistry 2015Genetically encoded optical tools have revolutionized modern biology by allowing detection and control of biological processes with exceptional spatiotemporal precision... (Review)
Review
Genetically encoded optical tools have revolutionized modern biology by allowing detection and control of biological processes with exceptional spatiotemporal precision and sensitivity. Natural photoreceptors provide researchers with a vast source of molecular templates for engineering of fluorescent proteins, biosensors, and optogenetic tools. Here, we give a brief overview of natural photoreceptors and their mechanisms of action. We then discuss fluorescent proteins and biosensors developed from light-oxygen-voltage-sensing (LOV) domains and phytochromes, as well as their properties and applications. These fluorescent tools possess unique characteristics not achievable with green fluorescent protein-like probes, including near-infrared fluorescence, independence of oxygen, small size, and photosensitizer activity. We next provide an overview of available optogenetic tools of various origins, such as LOV and BLUF (blue-light-utilizing flavin adenine dinucleotide) domains, cryptochromes, and phytochromes, enabling control of versatile cellular processes. We analyze the principles of their function and practical requirements for use. We focus mainly on optical tools with demonstrated use beyond bacteria, with a specific emphasis on their applications in mammalian cells.
Topics: Arabidopsis; Biosensing Techniques; Deinococcus; Luminescent Proteins; Optogenetics; Phytochrome; Protein Engineering; Rhodopseudomonas
PubMed: 25706899
DOI: 10.1146/annurev-biochem-060614-034411 -
The Journal of Biological Chemistry Jul 2020Fatty acids play many important roles in cells and also in industrial processes. Furan fatty acids (FuFAs) are present in the lipids of some plant, fish, and microbial...
Fatty acids play many important roles in cells and also in industrial processes. Furan fatty acids (FuFAs) are present in the lipids of some plant, fish, and microbial species and appear to function as second messengers in pathways that protect cells from membrane-damaging agents. We report here the results of chemical, genetic, and synthetic biology experiments to decipher the biosynthesis of the monomethylated FuFA, methyl 9-(3-methyl-5-pentylfuran-2-yl) nonanoate (9M5-FuFA), and its dimethyl counterpart, methyl 9-(3,4-dimethyl-5-pentylfuran-2-yl) nonanoate (9D5-FuFA), in two α-proteobacteria. Each of the steps in FuFA biosynthesis occurs on pre-existing phospholipid fatty acid chains, and we identified pathway intermediates and the gene products that catalyze 9M5-FuFA and 9D5-FuFA synthesis in 2.4.1 and CGA009. One previously unknown pathway intermediate was a methylated diunsaturated fatty acid, (1012)-11-methyloctadeca-10,12-dienoic acid (11Me-10,12-18:2), produced from (11)-methyloctadeca-11-enoic acid (11Me-12-18:1) by a newly identified fatty acid desaturase, UfaD. We also show that molecular oxygen (O) is the source of the oxygen atom in the furan ring of 9M5-FuFA, and our findings predict that an O-derived oxygen atom is incorporated into 9M5-FuFA via a protein, UfaO, that uses the 11Me-1012-18:2 fatty acid phospholipid chain as a substrate. We discovered that also contains a SAM-dependent methylase, FufM, that produces 9D5-FuFA from 9M5-FuFA. These results uncover the biochemical sequence of intermediates in a bacterial pathway for 9M5-FuFA and 9D5-FuFA biosynthesis and suggest the existence of homologs of the enzymes identified here that could function in FuFA biosynthesis in other organisms.
Topics: Biosynthetic Pathways; Fatty Acids; Furans; Rhodobacter sphaeroides; Rhodopseudomonas
PubMed: 32434926
DOI: 10.1074/jbc.RA120.013697 -
BMC Microbiology Dec 2018Pyrazosulfuron-ethyl is a long lasting herbicide in the agro-ecosystem and its residue is toxic to crops and other non-target organisms. A better understanding of...
BACKGROUND
Pyrazosulfuron-ethyl is a long lasting herbicide in the agro-ecosystem and its residue is toxic to crops and other non-target organisms. A better understanding of molecular basis in pyrazosulfuron-ethyl tolerant organisms will shed light on the adaptive mechanisms to this herbicide.
RESULTS
Pyrazosulfuron-ethyl inhibited biomass production in Rhodopseudomonas palustris PSB-S, altered cell morphology, suppressed flagella formation, and reduced pigment biosynthesis through significant suppression of carotenoids biosynthesis. A total of 1127 protein spots were detected in the two-dimensional gel electrophoresis. Among them, 72 spots representing 56 different proteins were found to be differently expressed using MALDI-TOF/TOF-MS, including 26 up- and 30 down-regulated proteins in the pyrazosulfuron-ethyl-treated PSB-S cells. The up-regulated proteins were involved predominantly in oxidative stress or energy generation pathways, while most of the down-regulated proteins were involved in the biomass biosynthesis pathway. The protein expression profiles suggested that the elongation factor G, cell division protein FtsZ, and proteins associated with the ABC transporters were crucial for R. palustris PSB-S tolerance against pyrazosulfuron-ethyl.
CONCLUSION
Up-regulated proteins, including elongation factor G, cell division FtsZ, ATP synthase, and superoxide dismutase, and down-regulated proteins, including ALS III and ABC transporters, as well as some unknown proteins might play roles in R. palustris PSB-S adaptation to pyrazosulfuron-ethyl induced stresses. Functional validations of these candidate proteins should help to develope transgenic crops resistant to pyrazosulfuron-ethyl.
Topics: Adaptation, Physiological; Bacterial Proteins; Carotenoids; Gene Expression Regulation, Bacterial; Herbicides; Pyrazoles; Pyrimidines; Rhodopseudomonas; Stress, Physiological
PubMed: 30526497
DOI: 10.1186/s12866-018-1361-y