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Literature summary extracted from

  • Tan, I.K.P.; Foong, C.P.; Tan, H.T.; Lim, H.; Zain, N.A.; Tan, Y.C.; Hoh, C.C.; Sudesh, K.
    Polyhydroxyalkanoate (PHA) synthase genes and PHA-associated gene clusters in Pseudomonas spp. and Janthinobacterium spp. isolated from Antarctica (2020), J. Biotechnol., 313, 18-28 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.3.1.304 cloning from the PHAC cluster, DNA and amino acid sequence determination and analysis, phylogenetic analysis, genotyping Pseudomonas sp. UMAB-08
2.3.1.304 cloning from the PHAC cluster, DNA and amino acid sequence determination and analysis, phylogenetic analysis, genotyping Pseudomonas sp. UMAB-40
2.3.1.304 cloning from the PHAC cluster, DNA and amino acid sequence determination and analysis, phylogenetic analysis, genotyping, functional recombinant heterologous expression in the PHA-negative mutant of Cupriavidus necator PHB-4 Janthinobacterium sp. UMAB-56
2.3.1.304 cloning from the PHAC cluster, DNA and amino acid sequence determination and analysis, phylogenetic analysis, genotyping, functional recombinant heterologous expression in the PHA-negative mutant of Cupriavidus necator PHB-4 Janthinobacterium sp. UMAB-60
2.3.1.304 cloning from the PHAC cluster, DNA and amino acid sequence determination and analysis, phylogenetic analysis, genotyping, recombinant expression in the PHA-negative mutant of Cupriavidus necator PHB-4 shows that the enzyme is not functional Janthinobacterium sp. UMAB-58
2.3.1.304 cloning from the PHAC cluster, DNA and amino acid sequence determination and analysis, phylogenetic analysis, genotyping, recombinant heterologous expression in the PHA-negative mutant of Cupriavidus necator PHB-4. PHB-4/pBBR1-ProCnJ60 accumulates 18.7% of wild-type polyhydroxybutyrate Janthinobacterium sp. UMAB-60

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
2.3.1.304 cytoplasm
-
 Janthinobacterium sp. UMAB-56 5737
-
2.3.1.304 cytoplasm
-
 Janthinobacterium sp. UMAB-60 5737
-
2.3.1.304 cytoplasm
-
 Pseudomonas sp. UMAB-08 5737
-
2.3.1.304 cytoplasm
-
 Pseudomonas sp. UMAB-40 5737
-

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.3.1.304 (R)-3-hydroxybutanoyl-CoA + [(R)-3-hydroxybutanoate]n Pseudomonas sp. UMAB-08
-
 [(R)-3-hydroxybutanoate](n+1) + CoA
-
 ?
2.3.1.304 (R)-3-hydroxybutanoyl-CoA + [(R)-3-hydroxybutanoate]n Pseudomonas sp. UMAB-40
-
 [(R)-3-hydroxybutanoate](n+1) + CoA
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.3.1.304 Janthinobacterium sp. UMAB-56
-
 isolated from Antarctica
-
2.3.1.304 Janthinobacterium sp. UMAB-58
-
 isolated from Antarctica
-
2.3.1.304 Janthinobacterium sp. UMAB-60
-
 isolated from Antarctica
-
2.3.1.304 Pseudomonas sp. UMAB-08
-
 isolated from Antarctica
-
2.3.1.304 Pseudomonas sp. UMAB-40
-
 isolated from Antarctica
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.3.1.304 (R)-3-hydroxybutanoyl-CoA + [(R)-3-hydroxybutanoate]n
-
 Pseudomonas sp. UMAB-08 [(R)-3-hydroxybutanoate](n+1) + CoA
-
 ?
2.3.1.304 (R)-3-hydroxybutanoyl-CoA + [(R)-3-hydroxybutanoate]n
-
 Pseudomonas sp. UMAB-40 [(R)-3-hydroxybutanoate](n+1) + CoA
-
 ?
2.3.1.304 additional information PHA biosynthesis and in vitro PhaC enzymatic assay results show that the uncharacterized putative PHA synthase from Janthinobacterium sp. UMAB-58 is not funtional Janthinobacterium sp. UMAB-58 ?
-
-
2.3.1.304 additional information PHA biosynthesis and in vitro PhaC enzymatic assay results show that the uncharacterized putative PHA synthase from Janthinobacterium sp. UMAB-60 is funtional Janthinobacterium sp. UMAB-60 ?
-
-

Synonyms

EC Number Synonyms Comment Organism
2.3.1.304 class I PHA synthase
-
 Janthinobacterium sp. UMAB-56
2.3.1.304 class I PHA synthase
-
 Janthinobacterium sp. UMAB-60
2.3.1.304 class I PHA synthase
-
 Pseudomonas sp. UMAB-08
2.3.1.304 class I PHA synthase
-
 Pseudomonas sp. UMAB-40
2.3.1.304 Class I PhaC
-
 Janthinobacterium sp. UMAB-56
2.3.1.304 Class I PhaC
-
 Janthinobacterium sp. UMAB-60
2.3.1.304 Class I PhaC
-
 Pseudomonas sp. UMAB-08
2.3.1.304 Class I PhaC
-
 Pseudomonas sp. UMAB-40
2.3.1.304 class II PHA synthase
-
 Pseudomonas sp. UMAB-08
2.3.1.304 class II PHA synthase
-
 Pseudomonas sp. UMAB-40
2.3.1.304 PHA synthase
-
 Janthinobacterium sp. UMAB-56
2.3.1.304 PHA synthase
-
 Janthinobacterium sp. UMAB-60
2.3.1.304 PHA synthase
-
 Pseudomonas sp. UMAB-08
2.3.1.304 PHA synthase
-
 Pseudomonas sp. UMAB-40
2.3.1.304 PHA synthase
-
 Janthinobacterium sp. UMAB-58
2.3.1.304 PhaC
-
 Janthinobacterium sp. UMAB-56
2.3.1.304 PhaC
-
 Janthinobacterium sp. UMAB-60
2.3.1.304 PhaC
-
 Pseudomonas sp. UMAB-08
2.3.1.304 PhaC
-
 Pseudomonas sp. UMAB-40
2.3.1.304 PhaC
-
 Janthinobacterium sp. UMAB-58
2.3.1.304 polyhydroxyalkanoate (PHA) synthase
-
 Pseudomonas sp. UMAB-08
2.3.1.304 polyhydroxyalkanoate (PHA) synthase
-
 Pseudomonas sp. UMAB-40
2.3.1.304 polyhydroxyalkanoate synthase
-
 Janthinobacterium sp. UMAB-56
2.3.1.304 polyhydroxyalkanoate synthase
-
 Janthinobacterium sp. UMAB-60
2.3.1.304 polyhydroxyalkanoate synthase
-
 Pseudomonas sp. UMAB-08
2.3.1.304 polyhydroxyalkanoate synthase
-
 Pseudomonas sp. UMAB-40
2.3.1.304 polyhydroxyalkanoate synthase
-
 Janthinobacterium sp. UMAB-58

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
2.3.1.304 20
-
 assay at Janthinobacterium sp. UMAB-56
2.3.1.304 20
-
 assay at Janthinobacterium sp. UMAB-60
2.3.1.304 20
-
 assay at Pseudomonas sp. UMAB-08
2.3.1.304 20
-
 assay at Pseudomonas sp. UMAB-40

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
2.3.1.304 7.8
-
 assay at Janthinobacterium sp. UMAB-56
2.3.1.304 7.8
-
 assay at Janthinobacterium sp. UMAB-60
2.3.1.304 7.8
-
 assay at Pseudomonas sp. UMAB-08
2.3.1.304 7.8
-
 assay at Pseudomonas sp. UMAB-40

General Information

EC Number General Information Comment Organism
2.3.1.304 evolution Pseudomonas isolates are found to carry PHA synthase genes which fall into two different PHA gene clusters, namely Class I and Class II, which are involved in the biosynthesis of short-chain-length-PHA (SCL-PHA) and medium-chain-length-PHA (MCL-PHA), respectively Pseudomonas sp. UMAB-08
2.3.1.304 evolution Pseudomonas isolates are found to carry PHA synthase genes which fall into two different PHA gene clusters, namely Class I and Class II, which are involved in the biosynthesis of short-chain-length-PHA (SCL-PHA) and medium-chain-length-PHA (MCL-PHA), respectively Pseudomonas sp. UMAB-40
2.3.1.304 evolution the Janthinobacterium isolates carry a Class I and an uncharacterized putative PHA synthase genes. No other gene involved in PHA synthesis is detected in close proximity to the uncharacterized putative PHA synthase gene in the Janthinobacterium isolates, therefore it falls into a separate clade from the ordinary Class I, II, III and IV clades of PHA synthase (PhaC) phylogenetic tree. Both of the antarctic Janthinobacterium isolates (UMAB-56 and UMAB-60) have a similar Class I PHA gene cluster as the Jantinobactarium spp. SCL-PHA producers Janthinobacterium sp. UMAB-56
2.3.1.304 evolution the Janthinobacterium isolates carry a Class I and an uncharacterized putative PHA synthase genes. No other gene involved in PHA synthesis is detected in close proximity to the uncharacterized putative PHA synthase gene in the Janthinobacterium isolates, therefore it falls into a separate clade from the ordinary Class I, II, III and IV clades of PHA synthase (PhaC) phylogenetic tree. Both of the antarctic Janthinobacterium isolates (UMAB-56 and UMAB-60) have a similar Class I PHA gene cluster as the Jantinobactarium spp. SCL-PHA producers Janthinobacterium sp. UMAB-60
2.3.1.304 evolution the Janthinobacterium isolates carry a Class I and an uncharacterized putative PHA synthase genes. The uncharacterized putative PHA synthase gene in the Janthinobacterium isolates falls into a separate clade from the ordinary Class I, II, III and IV clades of PHA synthase (PhaC) phylogenetic tree. Multiple sequence alignment shows that the uncharacterized putative PHA synthase gene contains all the highly conserved amino acid residues and the proposed catalytic triad of PHA synthase. Proposal of the uncharacterized PHA synthase as the new Class V PhaC Janthinobacterium sp. UMAB-60
2.3.1.304 evolution the Janthinobacterium isolates carry a Class I and an uncharacterized putative PHA synthase genes. The uncharacterized putative PHA synthase gene in the Janthinobacterium isolates falls into a separate clade from the ordinary Class I, II, III and IV clades of PHA synthase (PhaC) phylogenetic tree. Multiple sequence alignment shows that the uncharacterized putative PHA synthase gene contains all the highly conserved amino acid residues and the proposed catalytic triad of PHA synthase. Proposal of the uncharacterized PHA synthase as the new Class V PhaC Janthinobacterium sp. UMAB-58
2.3.1.304 physiological function Class I PHA synthases are involved in the biosynthesis of short-chain-length-polyhydroxyalkanoates (SCL-PHA) Janthinobacterium sp. UMAB-56
2.3.1.304 physiological function Class I PHA synthases are involved in the biosynthesis of short-chain-length-polyhydroxyalkanoates (SCL-PHA) Pseudomonas sp. UMAB-08
2.3.1.304 physiological function Class I PHA synthases are involved in the biosynthesis of short-chain-length-polyhydroxyalkanoates (SCL-PHA). The ability of UMAB-40 to produce SCL-MCL-PHA copolymers is likely due to the presence of both Class I and II PHA synthases in its genome Pseudomonas sp. UMAB-40
2.3.1.304 physiological function Class I PHA synthases are involved in the biosynthesis of short-chain-length-polyhydroxyalkanoates (SCL-PHA). The PHA produced by UMAB-60 is a homopolymer containing C4 repeating units Janthinobacterium sp. UMAB-60
2.3.1.304 physiological function Class II PHA synthases are involved in the biosynthesis of medium-chain-length-polyhydroxyalkanoates (MCL-PHA). Pseudomonas sp. UMAB-08 PHA gene cluster is very well conserved among the MCL-PHA producers Pseudomonas sp. UMAB-08
2.3.1.304 physiological function Class II PHA synthases are involved in the biosynthesis of medium-chain-length-polyhydroxyalkanoates (MCL-PHA). Pseudomonas sp. UMAB-08 PHA gene cluster is very well conserved among the MCL-PHA producers. Although UMAB-40 does not produce any homopolymer (PHA having only one type of monomeric unit), small peaks of the C4 position [3-hydroxybutyrate (3HB) monomer] in addition to larger peaks at C6 to C14 are detected. The ability of UMAB-40 to produce SCL-MCL-PHA copolymers is likely due to the presence of both Class I and II PHA synthases in its genome Pseudomonas sp. UMAB-40