Rhodobacter sphaeroides

Last updated

Rhodobacter sphaeroides
Scientific classification
Domain:
Bacteria
Phylum:
Pseudomonadota
Class:
Alphaproteobacteria
Order:
Rhodobacterales
Family:
Rhodobacteraceae
Genus:
Rhodobacter
Species:
R. sphaeroides
Binomial name
Rhodobacter sphaeroides
(van Niel, 1944) Imhoff et al., 1984

Rhodobacter sphaeroides is a kind of purple bacterium; a group of bacteria that can obtain energy through photosynthesis. Its best growth conditions are anaerobic phototrophy (photoheterotrophic and photoautotrophic) and aerobic chemoheterotrophy in the absence of light. [1] R. sphaeroides is also able to fix nitrogen. [2] It is remarkably metabolically diverse, as it is able to grow heterotrophically via fermentation and aerobic and anaerobic respiration. Such a metabolic versatility has motivated the investigation of R. sphaeroides as a microbial cell factory for biotechnological applications. [3]

Contents

Rhodobacter sphaeroides has been isolated from deep lakes and stagnant waters. [2]

Rhodobacter sphaeroides is one of the most pivotal organisms in the study of bacterial photosynthesis. It requires no unusual conditions for growth and is incredibly efficient. The regulation of its photosynthetic machinery is of great interest to researchers, as R. sphaeroides has an intricate system for sensing O2 tensions. [4] Also, when exposed to a reduction in the partial pressure of oxygen, R. sphaeroides develops invaginations in its cellular membrane. The photosynthetic apparatus is housed in these invaginations. [4] These invaginations are also known as chromatophores.

The genome of R. sphaeroides is also somewhat intriguing. It has two chromosomes, one of 3 Mb (CI) and one of 900 Kb (CII), and five naturally occurring plasmids. Many genes are duplicated between the two chromosomes but appear to be differentially regulated. Moreover, many of the open reading frames (ORFs) on CII seem to code for proteins of unknown function. When genes of unknown function on CII are disrupted, many types of auxotrophy result, emphasizing that the CII is not merely a truncated version of CI. [5]

Small non-coding RNA

Bacterial small RNAs have been identified as components of many regulatory networks. Twenty sRNAs were experimentally identified in Rhodobacter spheroides, and the abundant ones were shown to be affected by singlet oxygen (1O2) exposure. [6] 1O2 which generates photooxidative stress, is made by bacteriochlorophyll upon exposure to oxygen and light. One of the 1O2 induced sRNAs SorY (1O2 resistance RNA Y) was shown to be induced under several stress conditions and conferred resistance against 1O2 by affecting a metabolite transporter. [7] SorX is the second 1O2 induced sRNA that counteracts oxidative stress by targeting mRNA for a transporter. It also has an impact on resistance against organic hydroperoxides. [8] A cluster of four homologous sRNAs called CcsR for conserved CCUCCUCCC motif stress-induced RNA has been shown to play a role in photo-oxidative stress resistance as well. [9] PcrZ (photosynthesis control RNA Z) identified in R. sphaeroides, is a trans-acting sRNA which counteracts the redox-dependent induction of photosynthesis genes, mediated by protein regulators. [10]

Metabolism

R. sphaeroides encodes several terminal oxidases which allow electron transfer to oxygen and other electron acceptors (e.g. DMSO or TMAO). [11] Therefore, this microorganism can respire under oxic, micro-oxic and anoxic conditions under both light and dark conditions. Moreover, it is capable to accept a variety of carbon substrates, including C1 to C4 molecules, sugars and fatty acids. [12] Several pathways for glucose catabolism are present in its genome, such as the Embden–Meyerhof–Parnas pathway (EMP), the Entner–Doudoroff pathway (ED) and the Pentose phosphate pathway (PP). [13] The ED pathway is the predominant glycolytic pathway in this microorganism, [14] whereas the EMP pathway contributing only to a smaller extent. [15] Variation in nutrient availability has important effects on the physiology of this bacterium. For example, decrease in oxygen tensions activates the synthesis of photosynthetic machinery (including photosystems, antenna complexes and pigments). Moreover, depletion of nitrogen in the medium triggers intracellular accumulation of polyhydroxybutyrate, a reserve polymer. [16]

Biotechnological applications

A genome-scale metabolic model exists for this microorganism, [17] which can be used for predicting the effect of gene manipulations on its metabolic fluxes. For facilitating genome editing in this species, a CRISPR/Cas9 genome editing tool was developed [18] and expanded. [19] Moreover, partitioning of intracellular fluxes has been studied in detail, also with the help of 13C-glucose isotopomers. [15] [20] Altogether, these tools can be employed for improving R. sphaeroides as cell factory for industrial biotechnology. [3]

Knowledge of the physiology of R. sphaeroides allowed the development of biotechnological processes for the production of some endogenous compounds. These are hydrogen, polyhydroxybutyrate and isoprenoids (e.g. coenzyme Q10 and carotenoids). Moreover, this microorganism is used also for wastewater treatment. Hydrogen evolution occurs via the activity of the enzyme nitrogenase, [21] whereas isoprenoids are synthesized naturally via the endogenous MEP pathway. The native pathway has been optimized via genetic engineering for improving coenzyme Q10 synthesis. [22] Alternatively, improvement of isoprenoid synthesis was obtained via the introduction of a heterologous mevalonate pathway. [23] [16] Synthetic biology-driven engineering of the metabolism of R. sphaeroides, in combination to the functional replacement the MEP pathway with mevalonate pathway, [24] allowed to further increase bioproduction of isoprenoids in this species. [25]

Accepted name

Synonyms


Reclassification

In 2020 it was recommended that Rhodobacter sphaeroides be moved to the genus Cereibacter. [27] This is the name currently used by the NCBI taxonomy database.

Related Research Articles

<span class="mw-page-title-main">Metabolism</span> Set of chemical reactions in organisms

Metabolism is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cellular processes; the conversion of food to building blocks for proteins, lipids, nucleic acids, and some carbohydrates; and the elimination of metabolic wastes. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. The word metabolism can also refer to the sum of all chemical reactions that occur in living organisms, including digestion and the transportation of substances into and between different cells, in which case the above described set of reactions within the cells is called intermediary metabolism.

<span class="mw-page-title-main">Mevalonate pathway</span>

The mevalonate pathway, also known as the isoprenoid pathway or HMG-CoA reductase pathway is an essential metabolic pathway present in eukaryotes, archaea, and some bacteria. The pathway produces two five-carbon building blocks called isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), which are used to make isoprenoids, a diverse class of over 30,000 biomolecules such as cholesterol, vitamin K, coenzyme Q10, and all steroid hormones.

<span class="mw-page-title-main">Metagenomics</span> Study of genes found in the environment

Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microbiomics.

<span class="mw-page-title-main">Metabolic network modelling</span> Form of biological modelling

Metabolic network modelling, also known as metabolic network reconstruction or metabolic pathway analysis, allows for an in-depth insight into the molecular mechanisms of a particular organism. In particular, these models correlate the genome with molecular physiology. A reconstruction breaks down metabolic pathways into their respective reactions and enzymes, and analyzes them within the perspective of the entire network. In simplified terms, a reconstruction collects all of the relevant metabolic information of an organism and compiles it in a mathematical model. Validation and analysis of reconstructions can allow identification of key features of metabolism such as growth yield, resource distribution, network robustness, and gene essentiality. This knowledge can then be applied to create novel biotechnology.

An apicoplast is a derived non-photosynthetic plastid found in most Apicomplexa, including Toxoplasma gondii, and Plasmodium falciparum and other Plasmodium spp., but not in others such as Cryptosporidium. It originated from algae through secondary endosymbiosis; there is debate as to whether this was a green or red alga. The apicoplast is surrounded by four membranes within the outermost part of the endomembrane system. The apicoplast hosts important metabolic pathways like fatty acid synthesis, isoprenoid precursor synthesis and parts of the heme biosynthetic pathway.

The non-mevalonate pathway—also appearing as the mevalonate-independent pathway and the 2-C-methyl-D-erythritol 4-phosphate/1-deoxy-D-xylulose 5-phosphate (MEP/DOXP) pathway—is an alternative metabolic pathway for the biosynthesis of the isoprenoid precursors isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). The currently preferred name for this pathway is the MEP pathway, since MEP is the first committed metabolite on the route to IPP.

Fluxomics describes the various approaches that seek to determine the rates of metabolic reactions within a biological entity. While metabolomics can provide instantaneous information on the metabolites in a biological sample, metabolism is a dynamic process. The significance of fluxomics is that metabolic fluxes determine the cellular phenotype. It has the added advantage of being based on the metabolome which has fewer components than the genome or proteome.

Microbial biodegradation is the use of bioremediation and biotransformation methods to harness the naturally occurring ability of microbial xenobiotic metabolism to degrade, transform or accumulate environmental pollutants, including hydrocarbons, polychlorinated biphenyls (PCBs), polyaromatic hydrocarbons (PAHs), heterocyclic compounds, pharmaceutical substances, radionuclides and metals.

The enzyme phosphoketolase(EC 4.1.2.9) catalyzes the chemical reactions

<span class="mw-page-title-main">Archaea</span> Domain of single-celled organisms

Archaea is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this term has fallen out of use.

<i>Rhodopseudomonas palustris</i> Species of bacterium

Rhodopseudomonas palustris is a rod-shaped, Gram-negative purple nonsulfur bacterium, notable for its ability to switch between four different modes of metabolism.

Tryptophan-rich sensory proteins (TspO) are a family of proteins that are involved in transmembrane signalling. In either prokaryotes or mitochondria they are localized to the outer membrane, and have been shown to bind and transport dicarboxylic tetrapyrrole intermediates of the haem biosynthetic pathway. They are associated with the major outer membrane porins and with the voltage-dependent anion channel.

Rhodovulum sulfidophilum is a gram-negative purple nonsulfur bacteria. The cells are rod-shaped, and range in size from 0.6 to 0.9 μm wide and 0.9 to 2.0 μm long, and have a polar flagella. These cells reproduce asexually by binary fission. This bacterium can grow anaerobically when light is present, or aerobically (chemoheterotrophic) under dark conditions. It contains the photosynthetic pigments bacteriochlorophyll a and of carotenoids.

Chlorobaculum tepidum, previously known as Chlorobium tepidum, is an anaerobic, thermophilic green sulfur bacteria first isolated from New Zealand. Its cells are gram-negative and non-motile rods of variable length. They contain chlorosomes and bacteriochlorophyll a and c.

<span class="mw-page-title-main">Antonius Suwanto</span>

Antonius Suwanto, is an Indonesian biologist and professor, known for discovering two circular chromosomes or plasmids in Rhodobacter with Kaplan S in 1989.

Rhodobacter capsulatus is a species of purple bacteria, a group of bacteria that can obtain energy through photosynthesis. Its name is derived from the Latin adjective "capsulatus", itself derived Latin noun "capsula", and the associated Latin suffix for masculine nouns, "-atus".

Metabolite damage can occur through enzyme promiscuity or spontaneous chemical reactions. Many metabolites are chemically reactive and unstable and can react with other cell components or undergo unwanted modifications. Enzymatically or chemically damaged metabolites are always useless and often toxic. To prevent toxicity that can occur from the accumulation of damaged metabolites, organisms have damage-control systems that:

  1. Reconvert damaged metabolites to their original, undamaged form
  2. Convert a potentially harmful metabolite to a benign one
  3. Prevent damage from happening by limiting the build-up of reactive, but non-damaged metabolites that can lead to harmful products
<span class="mw-page-title-main">Chlorophyllide</span> Chemical compound

Chlorophyllide a and Chlorophyllide b are the biosynthetic precursors of chlorophyll a and chlorophyll b respectively. Their propionic acid groups are converted to phytyl esters by the enzyme chlorophyll synthase in the final step of the pathway. Thus the main interest in these chemical compounds has been in the study of chlorophyll biosynthesis in plants, algae and cyanobacteria. Chlorophyllide a is also an intermediate in the biosynthesis of bacteriochlorophylls.

<span class="mw-page-title-main">Chlorophyllide a reductase</span> Enzyme

Chlorophyllide a reductase (EC 1.3.7.15), also known as COR, is an enzyme with systematic name bacteriochlorophyllide-a:ferredoxin 7,8-oxidoreductase. It catalyses the following chemical reaction

<span class="mw-page-title-main">Markus Ralser</span> Italian biologist

Markus Ralser is an Italian biologist. His main research interest is metabolism of microorganisms. He is also known for his work on the origin of metabolism during the origin of life, and proteomics.

References

  1. ↑ Mackenzie C, Eraso JM, Choudhary M, Roh JH, Zeng X, Bruscella P, et al. (2007). "Postgenomic adventures with Rhodobacter sphaeroides". Annu Rev Microbiol. 61: 283–307. doi:10.1146/annurev.micro.61.080706.093402. PMID   17506668.
  2. 1 2 De Universiteit van Texas over Rhodobacter sphaeroides Archived 2009-07-10 at the Wayback Machine
  3. 1 2 Orsi E, Beekwilder J, Eggink G, Kengen SW, Weusthuis RA (2020). "The transition of Rhodobacter sphaeroides into a microbial cell factory". Biotechnology and Bioengineering. 118 (2): 531–541. doi: 10.1002/bit.27593 . PMC   7894463 . PMID   33038009.
  4. 1 2 Oh, JI.; Kaplan, S. (Mar 2001). "Generalized approach to the regulation and integration of gene expression". Mol Microbiol. 39 (5): 1116–23. doi: 10.1111/j.1365-2958.2001.02299.x . PMID   11251830. S2CID   27053575.
  5. ↑ Mackenzie, C; Simmons, AE; Kaplan, S (1999). "Multiple chromosomes in bacteria. The yin and yang of trp gene localization in Rhodobacter sphaeroides 2.4.1". Genetics. 153 (2): 525–38. doi:10.1093/genetics/153.2.525. PMC   1460784 . PMID   10511537.
  6. ↑ Berghoff, Bork A.; Glaeser, Jens; Sharma, Cynthia M.; Vogel, Jörg; Klug, Gabriele (2009-12-01). "Photooxidative stress-induced and abundant small RNAs in Rhodobacter sphaeroides". Molecular Microbiology. 74 (6): 1497–1512. doi: 10.1111/j.1365-2958.2009.06949.x . ISSN   1365-2958. PMID   19906181.
  7. ↑ Adnan, Fazal; Weber, Lennart; Klug, Gabriele (2015-01-01). "The sRNA SorY confers resistance during photooxidative stress by affecting a metabolite transporter in Rhodobacter sphaeroides". RNA Biology. 12 (5): 569–577. doi:10.1080/15476286.2015.1031948. ISSN   1555-8584. PMC   4615379 . PMID   25833751.
  8. ↑ Peng, Tao; Berghoff, Bork A.; Oh, Jeong-Il; Weber, Lennart; Schirmer, Jasmin; Schwarz, Johannes; Glaeser, Jens; Klug, Gabriele (2016-10-02). "Regulation of a polyamine transporter by the conserved 3' UTR-derived sRNA SorX confers resistance to singlet oxygen and organic hydroperoxides in Rhodobacter sphaeroides". RNA Biology. 13 (10): 988–999. doi:10.1080/15476286.2016.1212152. ISSN   1555-8584. PMC   5056773 . PMID   27420112.
  9. ↑ Billenkamp, Fabian; Peng, Tao; Berghoff, Bork A.; Klug, Gabriele (May 2015). "A cluster of four homologous small RNAs modulates C1 metabolism and the pyruvate dehydrogenase complex in Rhodobacter sphaeroides under various stress conditions". Journal of Bacteriology. 197 (10): 1839–1852. doi:10.1128/JB.02475-14. ISSN   1098-5530. PMC   4402390 . PMID   25777678.
  10. ↑ Mank, Nils N.; Berghoff, Bork A.; Hermanns, Yannick N.; Klug, Gabriele (2012-10-02). "Regulation of bacterial photosynthesis genes by the small noncoding RNA PcrZ". Proceedings of the National Academy of Sciences of the United States of America. 109 (40): 16306–16311. Bibcode:2012PNAS..10916306M. doi: 10.1073/pnas.1207067109 . ISSN   1091-6490. PMC   3479615 . PMID   22988125.
  11. ↑ Zannoni D, Schoepp-Cothenet B, Hosler J (2013). "Respiration and Respiratory Complexes". The Purple Phototrophic Bacteria. 28: 537–561. doi: 10.1186/1752-0509-7-89 . ISSN   1752-0509. PMC   3849096 . PMID   24034347.
  12. ↑ Tabita FR (2004). "The Biochemistry and Metabolic Regulation of Carbon Metabolism and CO2 Fixation in Purple Bacteria". Anoxygenic Photosynthetic Bacteria. Advances in Photosynthesis and Respiration. 2: 885–914. doi:10.1007/0-306-47954-0_41. ISBN   0-7923-3681-X.
  13. ↑ Imam S, Noguera D, Donohue T. "Global insights into energetic and metabolic networks in Rhodobacter sphaeroides". BMC Systems Biology. 7 (1): 89. doi:10.1007/0-306-47954-0_41.
  14. ↑ Fuhrer T, Fischer E, Sauer U (2005). "Experimental Identification and Quantification of Glucose Metabolism in Seven Bacterial Species". Journal of Bacteriology. 187 (5): 1581–1590. doi: 10.1128/JB.187.5.1581-1590.2005 . ISSN   0021-9193. PMC   1064017 . PMID   15716428.
  15. 1 2 Orsi E, Beekwilder J, Peek S, Eggink G, Kengen SW, Weusthuis RA (2020). "Metabolic flux ratio analysis by parallel 13C labeling of isoprenoid biosynthesis in Rhodobacter sphaeroides". Metabolic Engineering. 57: 228–238. doi: 10.1016/j.ymben.2019.12.004 . PMID   31843486.
  16. 1 2 Orsi E, Folch PL, Monje-Lopez V, Fernhout BM, Turcato A, Kengen SW, Eggink G, Weusthuis RA (2019). "Characterization of heterotrophic growth and sesquiterpene production by Rhodobacter sphaeroides on a defined medium". Journal of Industrial Microbiology & Biotechnology. 46 (8): 1179–1190. doi: 10.1007/s10295-019-02201-6 . PMC   6697705 . PMID   31187318.
  17. ↑ Imam S, Ylmaz S, Sohmen U, Gorzalski AS, Reed JL, Noguera DR, Donohue TJ (2011). "iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network". BMC Systems Biology. 5: 116. doi: 10.1186/1752-0509-5-116 . PMC   3152904 . PMID   21777427.
  18. ↑ Mougiakos I, Orsi E, Rifqi-Ghiffary M, Post W, De Maria A, Adiego-Perez B, Kengen SW, Weusthuis RA, van der Oost J (2019). "Efficient Cas9-based genome editing of Rhodobacter sphaeroides for metabolic engineering". Microbial Cell Factories. 18 (1): 204. doi: 10.1186/s12934-019-1255-1 . PMC   6876111 . PMID   31767004.
  19. ↑ Luo Y, Ge M, Wang B, Sun C, Wang J, Dong Y, Xi JJ (2020). "CRISPR/Cas9-deaminase enables robust base editing in Rhodobacter sphaeroides 2.4.1". Microbial Cell Factories. 19 (1): 93. doi: 10.1186/s12934-020-01345-w . PMC   7183636 . PMID   32334589.
  20. ↑ Tao Y, Liu D, Yan X, Zhou Z, Lee JK, Yang C (2012). "Network Identification and Flux Quantification of Glucose Metabolism in Rhodobacter sphaeroides under Photoheterotrophic H2-Producing Conditions". Journal of Bacteriology. 194 (2): 274–283. doi: 10.1128/JB.05624-11 . PMC   3256653 . PMID   22056932.
  21. ↑ Luo Y, Ge M, Wang B, Sun C, Wang J, Dong Y, Xi JJ (2002). "Aspects of the metabolism of hydrogen production by Rhodobacter sphaeroides". International Journal of Hydrogen Energy. 27 (11–12): 1315–1329. doi: 10.1016/S0360-3199(02)00127-1 .
  22. ↑ Lu W, Ye L, Xu H, Xe W, Gu J, Yu H (2013). "Enhanced production of coenzyme Q10 by self‐regulating the engineered MEP pathway in Rhodobacter sphaeroides". Biotechnology and Bioengineering. 111 (4): 761–769. doi:10.1002/bit.25130. PMID   24122603. S2CID   205503575.
  23. ↑ Beekwilder J, van Houwelingen A, Cankar K, van Dijk AD, de Jong RM, Stoopen G, Bouwmeester H, Achkar J, Sonke T, Bosch D (2013). "Valencene synthase from the heartwook of Nootka cyperss (Callitropsis nootkatensis) for biotechnological production of valencene". BMC Systems Biology. 12 (2): 174–182. doi: 10.1111/pbi.12124 . PMID   24112147.
  24. ↑ Orsi E, Beekwilder J, van Gelder D, van Houwelingen A, Eggink G, Kengen SW, Weusthuis RA (2020). "Functional replacement of isoprenoid pathways in Rhodobacter sphaeroides". Microbial Biotechnology. 13 (4): 1082–1093. doi: 10.1111/1751-7915.13562 . PMC   7264872 . PMID   32207882.
  25. ↑ Orsi E, Mougiakos I, Post W, Beekwilder J, Dompe M, Eggink G, van der Oost J, Kengen SW, Weusthuis RA (2020). "Growth-uncoupled isoprenoid synthesis in Rhodobacter sphaeroides". Biotechnology for Biofuels. 13: 123. doi: 10.1186/s13068-020-01765-1 . PMC   7359475 . PMID   32684976.
  26. ↑ Bacteriology Insight Orienting System over Rhodobacter sphaeroides [ permanent dead link ]
  27. ↑ Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M (2020). "Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria". Frontiers in Microbiology. 11: 468. doi: 10.3389/fmicb.2020.00468 . PMC   7179689 . PMID   32373076.

Bibliography

This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.