Literature summary for 4.2.1.90 extracted from

Khosravi, C.; Kun, R.S.; Visser, J.; Aguilar-Pontes, M.V.; de Vries, R.P.; Battaglia, E.
In vivo functional analysis of L-rhamnose metabolic pathway in Aspergillus niger a tool to identify the potential inducer of RhaR (2017), BMC Microbiol., 17, 214-227 .

Cloned(Commentary)

Cloned (Comment)	Organism
gene LRA3, genetic organization, L-rhamnose catabolism genes RHA1, LRA2, LRA3 and LRA4 are organized in a chromosomal gene cluster in Scheffersomyces stipitis. In Scheffersomyces stipitis, another transcription factor than TRC1 is found in the L-rhamnose cluster, FST14. This transcription factor is more up-regulated than TRC1 on L-rhamnose and it might be co-regulating the pectinolytic genes together with TRC1	Scheffersomyces stipitis
gene lraC, genetic organization, genes lraA, lraB and lraC, as well as the L-rhamnose regulator RhaR are organized in a cluster	Aspergillus niger

Cloned (Comment)

Organism

gene LRA3, genetic organization, L-rhamnose catabolism genes RHA1, LRA2, LRA3 and LRA4 are organized in a chromosomal gene cluster in Scheffersomyces stipitis. In Scheffersomyces stipitis, another transcription factor than TRC1 is found in the L-rhamnose cluster, FST14. This transcription factor is more up-regulated than TRC1 on L-rhamnose and it might be co-regulating the pectinolytic genes together with TRC1

Scheffersomyces stipitis

gene lraC, genetic organization, genes lraA, lraB and lraC, as well as the L-rhamnose regulator RhaR are organized in a cluster

Aspergillus niger

Protein Variants

Protein Variants	Comment	Organism
additional information	construction of a DELTAlraC knockout mutant from strain CBS 141257, gene deletion and transcriptomic analysis is performed to elucidate the function of LraC, protoplast-mediated transformations of Aspergillus niger. Deletion of genes lraA, lraB or lraC causes a reduction in expression level of the other genes of the L-rhamnose pathway. Strongly reduced expression levels of lraA, lraB, rhaR, rglB, rgxA and rgaeA are observed in the DELTAlraC mutant upon the 2 h transfer to L-rhamnonate compared to the reference strain. But none of the deletions of genes lraA, lraB or lraC results in accumulation of the inducer of the pathway regulator (RhaR)	Aspergillus niger

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
L-rhamnonate	Aspergillus niger	-	2-dehydro-3-deoxy-L-rhamnonate + H2O	-	?
L-rhamnonate	Scheffersomyces stipitis	-	2-dehydro-3-deoxy-L-rhamnonate + H2O	-	?
L-rhamnonate	Scheffersomyces stipitis ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545	-	2-dehydro-3-deoxy-L-rhamnonate + H2O	-	?
L-rhamnonate	Aspergillus niger CBS 141257	-	2-dehydro-3-deoxy-L-rhamnonate + H2O	-	?

Organism

Organism	UniProt	Comment	Textmining
Aspergillus niger	-	the CBS 141257 strain is obtained by transformation of strain N593.20 with uridine (pyrG) from Aspergillus oryzae	-
Aspergillus niger CBS 141257	-	the CBS 141257 strain is obtained by transformation of strain N593.20 with uridine (pyrG) from Aspergillus oryzae	-
Scheffersomyces stipitis	A3LZU6	i.e. Pichia stipitis	-
Scheffersomyces stipitis ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545	A3LZU6	i.e. Pichia stipitis	-

Source Tissue

Source Tissue	Comment	Organism	Textmining
mycelium	-	Aspergillus niger	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
L-rhamnonate	-	Aspergillus niger	2-dehydro-3-deoxy-L-rhamnonate + H2O	-	?
L-rhamnonate	-	Scheffersomyces stipitis	2-dehydro-3-deoxy-L-rhamnonate + H2O	-	?
L-rhamnonate	-	Scheffersomyces stipitis ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545	2-dehydro-3-deoxy-L-rhamnonate + H2O	-	?
L-rhamnonate	-	Aspergillus niger CBS 141257	2-dehydro-3-deoxy-L-rhamnonate + H2O	-	?

Synonyms

Synonyms	Comment	Organism
LRA3	-	Scheffersomyces stipitis
LraC	-	Aspergillus niger
PICST_50672	-	Scheffersomyces stipitis

General Information

General Information	Comment	Organism
malfunction	a double deletion of lraC and lraA in Aspergillus niger results in a strain that exhibits no L-rhamnose dehydrogenase activity and cannot consume or grow on L-rhamnose. Deletion of the clustered genes lraA, lraB or lraC causes a reduction in expression level of the other genes of the L-rhamnose pathway, rhtA is not expressed in the DELTAlraC and DELATrhaR mutants. Strongly reduced expression levels of lraA, lraB, rhaR, rglB, rgxA and rgaeA are observed in the DELTAlraC mutant upon the 2 h transfer to L-rhamnonate compared to the reference strain	Aspergillus niger
metabolism	L-rhamnonate dehydratase (LRA3) converts L-rhamnonate to 2-dehydro-3-deoxy-L-rhamnonate (L-KDR), catalyzing the third step of the non-phosphorylative pathway in Schefferomyces stipitis. The inducer of RhaR is beyond L-rhamnonate dehydratase (LraC) and is likely to be the 2-keto-3-L-deoxyrhamnonate	Scheffersomyces stipitis
metabolism	L-rhamnonate dehydratase (LraC) probably converts L-rhamnonate to 2-dehydro-3-deoxy-L-rhamnonate (L-KDR), catalyzing the third step of the non-phosphorylative pathway. The inducer of RhaR is beyond L-rhamnonate dehydratase (LraC) and is likely to be the 2-keto-3-L-deoxyrhamnonate	Aspergillus niger