scholarly journals Structure-Guided Expansion of the Substrate Range of Methylmalonyl Coenzyme A Synthetase (MatB) of Rhodopseudomonas palustris

2012 ◽  
Vol 78 (18) ◽  
pp. 6619-6629 ◽  
Author(s):  
Heidi A. Crosby ◽  
Katherine C. Rank ◽  
Ivan Rayment ◽  
Jorge C. Escalante-Semerena
Keyword(s):  
Coenzyme A ◽  
Rhodopseudomonas Palustris ◽  
Photosynthetic Bacterium ◽  
Polyketide Biosynthesis ◽  
Content Type ◽  
Malonyl Coa ◽  
Purple Photosynthetic Bacterium ◽  
Important Building Block ◽  
Prime Target ◽  
Resolution Structure

ABSTRACTMalonyl coenzyme A (malonyl-CoA) and methylmalonyl-CoA are two of the most commonly used extender units for polyketide biosynthesis and are utilized to synthesize a vast array of pharmaceutically relevant products with antibacterial, antiparasitic, anticholesterol, anticancer, antifungal, and immunosuppressive properties. Heterologous hosts used for polyketide production such asEscherichia colioften do not produce significant amounts of methylmalonyl-CoA, however, requiring the introduction of other pathways for the generation of this important building block. Recently, the bacterial malonyl-CoA synthetase class of enzymes has been utilized to generate malonyl-CoA and methylmalonyl-CoA directly from malonate and methylmalonate. We demonstrate that in the purple photosynthetic bacteriumRhodopseudomonas palustris, MatB (RpMatB) acts as a methylmalonyl-CoA synthetase and is required for growth on methylmalonate. We report theapo(1.7-Å resolution) and ATP-bound (2.0-Å resolution) structure and kinetic analysis ofRpMatB, which shows similar activities for both malonate and methylmalonate, making it an ideal enzyme for heterologous polyketide biosynthesis. Additionally, rational, structure-based mutagenesis of the active site ofRpMatB led to substantially higher activity with ethylmalonate and butylmalonate, demonstrating that this enzyme is a prime target for expanded substrate specificity.

scholarly journals Draft Whole-Genome Sequence of the Purple Photosynthetic Bacterium Rhodopseudomonas palustris XCP

2018 ◽  
Vol 7 (4) ◽  
Author(s):  
Amiera Rayyan ◽  
Terry Meyer ◽  
John Kyndt
Keyword(s):  
Genome Sequence ◽  
Rhodopseudomonas Palustris ◽  
Photosynthetic Bacterium ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Wide Range ◽  
Purple Photosynthetic Bacterium

Rhodopseudomonas palustris is known for its versatile metabolic capabilities and has been proposed for a wide range of innovative applications. Here, we report the genome sequence of strain XCP, as well as a whole-genome nucleotide comparison of R. palustris strains, which indicates the need for further differentiation of the known strains.

scholarly journals A Disjointed Pathway for Malonate Degradation by Rhodopseudomonas palustris

2020 ◽  
Vol 86 (11) ◽  
Author(s):  
Zhaobao Wang ◽  
Qifeng Wen ◽  
Caroline S. Harwood ◽  
Bo Liang ◽  
Jianming Yang
Keyword(s):  
Carbon Source ◽  
Dicarboxylic Acid ◽  
Slow Growth ◽  
Rhodopseudomonas Palustris ◽  
Carbon Sources ◽  
Value Added ◽  
Poor Growth ◽  
Content Type ◽  
Phototrophic Bacterium ◽  
Malonyl Coa

ABSTRACT The purple nonsulfur phototrophic bacterium Rhodopseudomonas palustris strain CGA009 uses the three-carbon dicarboxylic acid malonate as the sole carbon source under phototrophic conditions. However, this bacterium grows extremely slowly on this compound and does not have operons for the two pathways for malonate degradation that have been detected in other bacteria. Many bacteria grow on a spectrum of carbon sources, some of which are classified as poor growth substrates because they support low growth rates. This trait is rarely addressed in the literature, but slow growth is potentially useful in biotechnological applications where it is imperative for bacteria to divert cellular resources to value-added products rather than to growth. This prompted us to explore the genetic and physiological basis for the slow growth of R. palustris with malonate as a carbon source. There are two unlinked genes annotated as encoding a malonyl coenzyme A (malonyl-CoA) synthetase (MatB) and a malonyl-CoA decarboxylase (MatA) in the genome of R. palustris, which we verified as having the predicted functions. Additionally, two tripartite ATP-independent periplasmic transporters (TRAP systems) encoded by rpa2047 to rpa2049 and rpa2541 to rpa2543 were needed for optimal growth on malonate. Most of these genes were expressed constitutively during growth on several carbon sources, including malonate. Our data indicate that R. palustris uses a piecemeal approach to growing on malonate. The data also raise the possibility that this bacterium will evolve to use malonate efficiently if confronted with an appropriate selection pressure. IMPORTANCE There is interest in understanding how bacteria metabolize malonate because this three-carbon dicarboxylic acid can serve as a building block in bioengineering applications to generate useful compounds that have an odd number of carbons. We found that the phototrophic bacterium Rhodopseudomonas palustris grows extremely slowly on malonate. We identified two enzymes and two TRAP transporters involved in the uptake and metabolism of malonate, but some of these elements are apparently not very efficient. R. palustris cells growing with malonate have the potential to be excellent biocatalysts, because cells would be able to divert cellular resources to the production of value-added compounds instead of using them to support rapid growth. In addition, our results suggest that R. palustris is a candidate for directed evolution studies to improve growth on malonate and to observe the kinds of genetic adaptations that occur to make a metabolic pathway operate more efficiently.

scholarly journals Draft Whole-Genome Sequence of the Purple Nonsulfur Photosynthetic Bacterium Rhodopseudomonas rutila R1

2018 ◽  
Vol 7 (15) ◽  
Author(s):  
Sydney Robertson ◽  
Amiera Rayyan ◽  
Terry Meyer ◽  
John Kyndt
Keyword(s):  
Genome Sequence ◽  
Type Strain ◽  
Rhodopseudomonas Palustris ◽  
Photosynthetic Bacterium ◽  
Whole Genome Sequence ◽  
Species Differentiation ◽  
Whole Genome ◽  
Purple Nonsulfur Bacteria ◽  
Content Type

Rhodopseudomonas species are purple nonsulfur bacteria found in many environments and known for their diverse metabolic capabilities. Here, we report the genome sequence of Rhodopseudomonas rutila type strain R1 and a whole-genome nucleotide comparison of related Rhodopseudomonas palustris species, suggesting the necessity for future reevaluation of the Rhodopseudomonas species differentiation.

scholarly journals Genome Sequence of the Unusual Purple Photosynthetic Bacterium Phaeovibrio sulfidiphilus, Only Distantly Related to Rhodospirillaceae, Reveals Unique Genes for Respiratory Nitrate Reduction and Glycerol Metabolism

2020 ◽  
Vol 9 (49) ◽  
Author(s):  
S. Dubey ◽  
T. E. Meyer ◽  
J. A. Kyndt
Keyword(s):  
Nitrate Reduction ◽  
Photosynthetic Bacteria ◽  
Photosynthetic Bacterium ◽  
Gene Clusters ◽  
Glycerol Metabolism ◽  
Freshwater Species ◽  
Content Type ◽  
Purple Photosynthetic Bacteria ◽  
Purple Photosynthetic Bacterium ◽  
Unique Genes

ABSTRACT Phaeovibrio sulfidiphilus was reported to be a divergent member of the purple photosynthetic bacteria with limited ability to metabolize organic compounds. Whole-genome-based analysis shows that it is indeed only distantly related to freshwater species of Rhodospirillaceae. Unexpectedly, the genome contains unique gene clusters for potential respiratory nitrate reduction and anaerobic glycerol metabolism.

scholarly journals The light intensity under which cells are grown controls the type of peripheral light-harvesting complexes that are assembled in a purple photosynthetic bacterium

2011 ◽  
Vol 440 (1) ◽  
pp. 51-61 ◽  
Author(s):  
Tatas H. P. Brotosudarmo ◽  
Aaron M. Collins ◽  
Andrew Gall ◽  
Aleksander W. Roszak ◽  
Alastair T. Gardiner ◽  
...  
Keyword(s):  
Light Intensity ◽  
Light Harvesting ◽  
Rhodopseudomonas Palustris ◽  
Photosynthetic Bacterium ◽  
Low Light ◽  
Light Harvesting Complexes ◽  
Density Maps ◽  
Purple Photosynthetic Bacterium ◽  
Resonance Raman Spectra ◽  
Apoprotein Composition

The differing composition of LH2 (peripheral light-harvesting) complexes present in Rhodopseudomonas palustris 2.1.6 have been investigated when cells are grown under progressively decreasing light intensity. Detailed analysis of their absorption spectra reveals that there must be more than two types of LH2 complexes present. Purified HL (high-light) and LL (low-light) LH2 complexes have mixed apoprotein compositions. The HL complexes contain PucABa and PucABb apoproteins. The LL complexes contain PucABa, PucABd and PucBb-only apoproteins. This mixed apoprotein composition can explain their resonance Raman spectra. Crystallographic studies and molecular sieve chromatography suggest that both the HL and the LL complexes are nonameric. Furthermore, the electron-density maps do not support the existence of an additional Bchl (bacteriochlorophyll) molecule; rather the density is attributed to the N-termini of the α-polypeptide.

scholarly journals Improving Production of Malonyl Coenzyme A-Derived Metabolites by Abolishing Snf1-Dependent Regulation of Acc1

mBio ◽  
2014 ◽  
Vol 5 (3) ◽  
Author(s):  
Shuobo Shi ◽  
Yun Chen ◽  
Verena Siewers ◽  
Jens Nielsen
Keyword(s):  
Fatty Acid ◽  
Coenzyme A ◽  
Fatty Acid Ethyl Esters ◽  
Ethyl Esters ◽  
Regulation Of Transcription ◽  
Acetyl Coa ◽  
Content Type ◽  
Obesity And Diabetes ◽  
Malonyl Coa ◽  
Hydroxypropionic Acid

ABSTRACT Acetyl coenzyme A (acetyl-CoA) carboxylase (ACCase) plays a central role in carbon metabolism and has been the site of action for the development of therapeutics or herbicides, as its product, malonyl-CoA, is a precursor for production of fatty acids and other compounds. Control of Acc1 activity in the yeast Saccharomyces cerevisiae occurs mainly at two levels, i.e., regulation of transcription and repression by Snf1 protein kinase at the protein level. Here, we demonstrate a strategy for improving the activity of ACCase in S. cerevisiae by abolishing posttranslational regulation of Acc1 via site-directed mutagenesis. It was found that introduction of two site mutations in Acc1, Ser659 and Ser1157, resulted in an enhanced activity of Acc1 and increased total fatty acid content. As Snf1 regulation of Acc1 is particularly active under glucose-limited conditions, we evaluated the effect of the two site mutations in chemostat cultures. Finally, we showed that our modifications of Acc1 could enhance the supply of malonyl-CoA and therefore successfully increase the production of two industrially important products derived from malonyl-CoA, fatty acid ethyl esters and 3-hydroxypropionic acid. IMPORTANCE ACCase is responsible for carboxylation of acetyl-CoA to produce malonyl-CoA, which is a crucial step in the control of fatty acid metabolism. ACCase opened the door for pharmaceutical treatments of obesity and diabetes as well as the development of new herbicides. ACCase is also recognized as a promising target for developing cell factories, as its malonyl-CoA product serves as a universal precursor for a variety of high-value compounds in white biotechnology. Yeast ACCase is a good model in understanding the enzyme’s catalysis, regulation, and inhibition. The present study describes the importance of protein phosphorylation in regulation of yeast ACCase and identifies potential regulation sites. This study led to the generation of a more efficient ACCase, which was applied in the production of two high-value compounds derived from malonyl-CoA, i.e., fatty acid ethyl esters that can be used as biodiesel and 3-hydroxypropionic acid that is considered an important platform chemical.

scholarly journals Structure, Activity, and Inhibition of the Carboxyltransferase β-Subunit of Acetyl Coenzyme A Carboxylase (AccD6) from Mycobacterium tuberculosis

2014 ◽  
Vol 58 (10) ◽  
pp. 6122-6132 ◽  
Author(s):  
Manchi C. M. Reddy ◽  
Ardala Breda ◽  
John B. Bruning ◽  
Mukul Sherekar ◽  
Spandana Valluru ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Fatty Acid Biosynthesis ◽  
Coenzyme A ◽  
Cell Activity ◽  
Acetyl Coa ◽  
Acetyl Coenzyme A ◽  
Content Type ◽  
Acetyl Coenzyme ◽  
Malonyl Coa

ABSTRACTInMycobacterium tuberculosis, the carboxylation of acetyl coenzyme A (acetyl-CoA) to produce malonyl-CoA, a building block in long-chain fatty acid biosynthesis, is catalyzed by two enzymes working sequentially: a biotin carboxylase (AccA) and a carboxyltransferase (AccD). While the exact roles of the three different biotin carboxylases (AccA1 to -3) and the six carboxyltransferases (AccD1 to -6) inM. tuberculosisare still not clear, AccD6 in complex with AccA3 can synthesize malonyl-CoA from acetyl-CoA. A series of 10 herbicides that target plant acetyl-CoA carboxylases (ACC) were tested for inhibition of AccD6 and for whole-cell activity againstM. tuberculosis. From the tested herbicides, haloxyfop, an arylophenoxypropionate, showedin vitroinhibition ofM. tuberculosisAccD6, with a 50% inhibitory concentration (IC50) of 21.4 ± 1 μM. Here, we report the crystal structures ofM. tuberculosisAccD6 in the apo form (3.0 Å) and in complex with haloxyfop-R(2.3 Å). The structure ofM. tuberculosisAccD6 in complex with haloxyfop-Rshows two molecules of the inhibitor bound on each AccD6 subunit. These results indicate the potential for developing novel therapeutics for tuberculosis based on herbicides with low human toxicity.

scholarly journals Structures of Rhodopseudomonas palustris RC-LH1 complexes with open or closed quinone channels

2021 ◽  
Vol 7 (3) ◽  
pp. eabe2631
Author(s):  
David J. K. Swainsbury ◽  
Pu Qian ◽  
Philip J. Jackson ◽  
Kaitlyn M. Faries ◽  
Dariusz M. Niedzwiedzki ◽  
...  
Keyword(s):  
Binding Sites ◽  
Rhodopseudomonas Palustris ◽  
Ring Closure ◽  
Light Harvesting Complex ◽  
The Core ◽  
Quinone Binding ◽  
Cryo Electron Microscopy ◽  
Unique Protein ◽  
Center Light ◽  
Resolution Structure

The reaction-center light-harvesting complex 1 (RC-LH1) is the core photosynthetic component in purple phototrophic bacteria. We present two cryo–electron microscopy structures of RC-LH1 complexes from Rhodopseudomonas palustris. A 2.65-Å resolution structure of the RC-LH114-W complex consists of an open 14-subunit LH1 ring surrounding the RC interrupted by protein-W, whereas the complex without protein-W at 2.80-Å resolution comprises an RC completely encircled by a closed, 16-subunit LH1 ring. Comparison of these structures provides insights into quinone dynamics within RC-LH1 complexes, including a previously unidentified conformational change upon quinone binding at the RC QB site, and the locations of accessory quinone binding sites that aid their delivery to the RC. The structurally unique protein-W prevents LH1 ring closure, creating a channel for accelerated quinone/quinol exchange.

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