Rhodobacter sphaeroides explained

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]

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.

Bibliography

External links

Notes and References

  1. Mackenzie C, Eraso JM, Choudhary M, Roh JH, Zeng X, Bruscella P, etal . Postgenomic adventures with Rhodobacter sphaeroides. . Annu Rev Microbiol . 2007 . 61 . 283–307 . 17506668 . 10.1146/annurev.micro.61.080706.093402.
  2. http://mmg.uth.tmc.edu/sphaeroides/introduction/introduction.html De Universiteit van Texas over Rhodobacter sphaeroides
  3. Orsi E, Beekwilder J, Eggink G, Kengen SW, Weusthuis RA . The transition of Rhodobacter sphaeroides into a microbial cell factory. . Biotechnology and Bioengineering . 2020 . 118 . 2 . 531–541 . 33038009 . 10.1002/bit.27593. 7894463 . free .
  4. Oh . JI. . Kaplan . S. . Generalized approach to the regulation and integration of gene expression. . Mol Microbiol . 39 . 5 . 1116–23 . Mar 2001 . 11251830 . 10.1111/j.1365-2958.2001.02299.x . 27053575 . free .
  5. 1460784 . 10511537 . 153 . Multiple chromosomes in bacteria. The yin and yang of trp gene localization in Rhodobacter sphaeroides 2.4.1 . Genetics . 525–38 . Mackenzie . C . Simmons . AE . Kaplan . S. 1999 . 2 . 10.1093/genetics/153.2.525 .
  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. 10.1111/j.1365-2958.2009.06949.x. 1365-2958. 19906181. free.
  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. 10.1080/15476286.2015.1031948. 1555-8584. 4615379. 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. 10.1080/15476286.2016.1212152. 1555-8584. 5056773. 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. 10.1128/JB.02475-14. 1098-5530. 4402390. 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. 10.1073/pnas.1207067109. 1091-6490. 3479615. 22988125. 2012PNAS..10916306M. free.
  11. Zannoni D, Schoepp-Cothenet B, Hosler J . Respiration and Respiratory Complexes. The Purple Phototrophic Bacteria . 2013. 28. 537–561. 10.1186/1752-0509-7-89. 1752-0509. 3849096. 24034347. free.
  12. Tabita FR. The Biochemistry and Metabolic Regulation of Carbon Metabolism and CO2 Fixation in Purple Bacteria. Anoxygenic Photosynthetic Bacteria. Advances in Photosynthesis and Respiration. 2004. 2. 885–914. 10.1007/0-306-47954-0_41. 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. 10.1007/0-306-47954-0_41.
  14. Fuhrer T, Fischer E, Sauer U . Experimental Identification and Quantification of Glucose Metabolism in Seven Bacterial Species. Journal of Bacteriology. 2005 . 187. 5. 1581–1590. 10.1128/JB.187.5.1581-1590.2005 . free . 0021-9193. 1064017. 15716428.
  15. Orsi E, Beekwilder J, Peek S, Eggink G, Kengen SW, Weusthuis RA . Metabolic flux ratio analysis by parallel 13C labeling of isoprenoid biosynthesis in Rhodobacter sphaeroides . Metabolic Engineering . 2020 . 57 . 228–238 . 31843486 . 10.1016/j.ymben.2019.12.004. free .
  16. Orsi E, Folch PL, Monje-Lopez V, Fernhout BM, Turcato A, Kengen SW, Eggink G, Weusthuis RA . Characterization of heterotrophic growth and sesquiterpene production by Rhodobacter sphaeroides on a defined medium . Journal of Industrial Microbiology & Biotechnology . 2019 . 46 . 8 . 1179–1190 . 31187318. 10.1007/s10295-019-02201-6. 6697705 . free .
  17. Imam S, Ylmaz S, Sohmen U, Gorzalski AS, Reed JL, Noguera DR, Donohue TJ . iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network. BMC Systems Biology . 2011 . 5. 116. 21777427. 10.1186/1752-0509-5-116. 3152904. free .
  18. Mougiakos I, Orsi E, Rifqi-Ghiffary M, Post W, De Maria A, Adiego-Perez B, Kengen SW, Weusthuis RA, van der Oost J . Efficient Cas9-based genome editing of Rhodobacter sphaeroides for metabolic engineering . Microbial Cell Factories . 2019 . 18 . 1 . 204 . 31767004. 10.1186/s12934-019-1255-1. 6876111 . free .
  19. Luo Y, Ge M, Wang B, Sun C, Wang J, Dong Y, Xi JJ . CRISPR/Cas9-deaminase enables robust base editing in Rhodobacter sphaeroides 2.4.1. Microbial Cell Factories . 2020 . 19. 1. 93. 32334589. 10.1186/s12934-020-01345-w . 7183636. free .
  20. Tao Y, Liu D, Yan X, Zhou Z, Lee JK, Yang C . Network Identification and Flux Quantification of Glucose Metabolism in Rhodobacter sphaeroides under Photoheterotrophic H2-Producing Conditions. Journal of Bacteriology. 2012. 194. 2. 274–283. 22056932. 10.1128/JB.05624-11. 3256653. free .
  21. Luo Y, Ge M, Wang B, Sun C, Wang J, Dong Y, Xi JJ . Aspects of the metabolism of hydrogen production by Rhodobacter sphaeroides . International Journal of Hydrogen Energy. 2002. 27 . 11–12 . 1315–1329 . 10.1016/S0360-3199(02)00127-1. free .
  22. Lu W, Ye L, Xu H, Xe W, Gu J, Yu H . Enhanced production of coenzyme Q10 by self‐regulating the engineered MEP pathway in Rhodobacter sphaeroides . Biotechnology and Bioengineering. 2013. 111 . 4 . 761–769 . 24122603. 10.1002/bit.25130. 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 . Valencene synthase from the heartwook of Nootka cyperss (Callitropsis nootkatensis) for biotechnological production of valencene . BMC Systems Biology . 2013 . 12 . 2 . 174–182 . 24112147. 10.1111/pbi.12124. free .
  24. Orsi E, Beekwilder J, van Gelder D, van Houwelingen A, Eggink G, Kengen SW, Weusthuis RA . Functional replacement of isoprenoid pathways in Rhodobacter sphaeroides . Microbial Biotechnology. 2020. 13 . 4 . 1082–1093 . 32207882. 10.1111/1751-7915.13562. 7264872 . free .
  25. Orsi E, Mougiakos I, Post W, Beekwilder J, Dompe M, Eggink G, van der Oost J, Kengen SW, Weusthuis RA . Growth-uncoupled isoprenoid synthesis in Rhodobacter sphaeroides . Biotechnology for Biofuels. 2020. 13 . 123 . 32684976. 10.1186/s13068-020-01765-1. 7359475 . free .
  26. http://www-sp2000ao.nies.go.jp/cgi-bin/bacteria.cgi?pno=6538 Bacteriology Insight Orienting System over Rhodobacter sphaeroides
  27. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria . Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M . Frontiers in Microbiology . 11. 468. 2020. 32373076. 7179689 . 10.3389/fmicb.2020.00468 . free .

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