Keyword search (4,163 papers available)

"transcriptomics" Keyword-tagged Publications:

Title Authors PubMed ID
1 A Bacteroides synthetic biology toolkit to build an in vivo malabsorption biosensor McCallum G; Burckhardt JC; He J; Hong A; Potvin-Trottier L; Tropini C; 41610848
BIOLOGY
2 An examination of the quinic acid utilization genes in Aspergillus niger reveals the involvement of two pH-dependent permeases Sgro M; Reid ID; Arentshorst M; Ram AFJ; Tsang A; 40853219
GENOMICS
3 em Candida albicans /em : a historical overview of investigations into an important human pathogen Shrivastava M; Whiteway M; 40522159
BIOLOGY
4 Transcriptomics identify the triggering of citrate export as the key event caused by manganese deficiency in Aspergillus niger Fekete E; Bíró V; Márton A; Bakondi-Kovács I; Sándor E; Kovács B; Geoffrion N; Tsang A; Kubicek CP; Karaffa L; 39377610
CSFG
5 Functional analysis of the protocatechuate branch of the β-ketoadipate pathway in Aspergillus niger Sgro M; Chow N; Olyaei F; Arentshorst M; Geoffrion N; Ram AFJ; Powlowski J; Tsang A; 37399977
BIOLOGY
6 Identification of Genes Involved in the Degradation of Lignocellulose Using Comparative Transcriptomics Gruninger RJ; Tsang A; McAllister TA; 37149538
CSFG
7 An Evolutionarily Conserved Transcriptional Activator-Repressor Module Controls Expression of Genes for D-Galacturonic Acid Utilization in Aspergillus niger. Niu J, Alazi E, Reid ID, Arentshorst M, Punt PJ, Visser J, Tsang A, Ram AF 28049705
CSFG
8 Identification of Genes Involved in the Degradation of Lignocellulose Using Comparative Transcriptomics. Gruninger RJ, Reid I, Forster RJ, Tsang A, McAllister TA 28417376
CSFG
9 Introduction: Overview of Fungal Genomics. de Vries RP, Grigoriev IV, Tsang A 29876804
CSFG

 

Title:Functional analysis of the protocatechuate branch of the β-ketoadipate pathway in Aspergillus niger
Authors:Sgro MChow NOlyaei FArentshorst MGeoffrion NRam AFJPowlowski JTsang A
Link:https://pubmed.ncbi.nlm.nih.gov/37399977/
DOI:10.1016/j.jbc.2023.105003
Publication:The Journal of biological chemistry
Keywords:3,4-dihydroxybenzoic acidAspergilluscatabolismenzyme kineticsfungigene knockoutprotocatechuic acidtranscriptomicsβ-ketoadipate
PMID:37399977 Category: Date Added:2023-07-04
Dept Affiliation: BIOLOGY
1 Department of Biology, Concordia University, Montreal, Quebec, Canada; Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada.
2 Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada.
3 Institute of Biology Leiden, Microbial Sciences, Leiden University, Leiden, The Netherlands.
4 Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada.
5 Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada; Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada.
6 Department of Biology, Concordia University, Montreal, Quebec, Canada; Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada. Electronic address: adrian.tsang@concordia.ca.

Description:

Bacteria and fungi catabolize plant-derived aromatic compounds by funneling into one of seven dihydroxylated aromatic intermediates, which then undergo ring fission and conversion to TCA cycle intermediates. Two of these intermediates, protocatechuic acid and catechol, converge on ß-ketoadipate which is further cleaved to succinyl-CoA and acetyl-CoA. These ß-ketoadipate pathways have been well characterized in bacteria. The corresponding knowledge of these pathways in fungi is incomplete. Characterization of these pathways in fungi would expand our knowledge and improve the valorization of lignin-derived compounds. Here, we used homology to characterize bacterial or fungal genes to predict the genes involved in the ß-ketoadipate pathway for protocatechuate utilization in the filamentous fungus Aspergillus niger. We further used the following approaches to refine the assignment of the pathway genes: whole transcriptome sequencing to reveal genes upregulated in the presence of protocatechuic acid; deletion of candidate genes to observe their ability to grow on protocatechuic acid; determination by mass spectrometry of metabolites accumulated by deletion mutants; and enzyme assays of the recombinant proteins encoded by candidate genes. Based on the aggregate experimental evidence, we assigned the genes for the five pathway enzymes as follows: NRRL3_01405 (prcA) encodes protocatechuate 3,4-dioxygenase; NRRL3_02586 (cmcA) encodes 3-carboxy-cis,cis-muconate cyclase; NRRL3_01409 (chdA) encodes 3-carboxymuconolactone hydrolase/decarboxylase; NRRL3_01886 (kstA) encodes ß-ketoadipate:succinyl-CoA transferase; and NRRL3_01526 (kctA) encodes ß-ketoadipyl-CoA thiolase. Strain carrying ?NRRL3_00837 could not grow on protocatechuic acid, suggesting that it is essential for protocatechuate catabolism. Its function is unknown as recombinant NRRL3_00837 did not affect the in vitro conversion of protocatechuic acid to ß-ketoadipate.





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