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Systems Biology of the qa Gene Cluster in Neurospora crassa

An ensemble of genetic networks that describe how the model fungal system, Neurospora crassa, utilizes quinic acid (QA) as a sole carbon source has been identified previously. A genetic network for QA metabolism involves the genes, qa-1F and qa-1S, that encode a transcriptional activator and repress...

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Autores principales: Tang, Xiaojia, Dong, Wubei, Griffith, James, Nilsen, Roger, Matthes, Allison, Cheng, Kevin B., Reeves, Jaxk, Schuttler, H.-Bernd, Case, Mary E., Arnold, Jonathan, Logan, David A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3114802/
https://www.ncbi.nlm.nih.gov/pubmed/21695121
http://dx.doi.org/10.1371/journal.pone.0020671
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author Tang, Xiaojia
Dong, Wubei
Griffith, James
Nilsen, Roger
Matthes, Allison
Cheng, Kevin B.
Reeves, Jaxk
Schuttler, H.-Bernd
Case, Mary E.
Arnold, Jonathan
Logan, David A.
author_facet Tang, Xiaojia
Dong, Wubei
Griffith, James
Nilsen, Roger
Matthes, Allison
Cheng, Kevin B.
Reeves, Jaxk
Schuttler, H.-Bernd
Case, Mary E.
Arnold, Jonathan
Logan, David A.
author_sort Tang, Xiaojia
collection PubMed
description An ensemble of genetic networks that describe how the model fungal system, Neurospora crassa, utilizes quinic acid (QA) as a sole carbon source has been identified previously. A genetic network for QA metabolism involves the genes, qa-1F and qa-1S, that encode a transcriptional activator and repressor, respectively and structural genes, qa-2, qa-3, qa-4, qa-x, and qa-y. By a series of 4 separate and independent, model-guided, microarray experiments a total of 50 genes are identified as QA-responsive and hypothesized to be under QA-1F control and/or the control of a second QA-responsive transcription factor (NCU03643) both in the fungal binuclear Zn(II)2Cys6 cluster family. QA-1F regulation is not sufficient to explain the quantitative variation in expression profiles of the 50 QA-responsive genes. QA-responsive genes include genes with products in 8 mutually connected metabolic pathways with 7 of them one step removed from the tricarboxylic (TCA) Cycle and with 7 of them one step removed from glycolysis: (1) starch and sucrose metabolism; (2) glycolysis/glucanogenesis; (3) TCA Cycle; (4) butanoate metabolism; (5) pyruvate metabolism; (6) aromatic amino acid and QA metabolism; (7) valine, leucine, and isoleucine degradation; and (8) transport of sugars and amino acids. Gene products both in aromatic amino acid and QA metabolism and transport show an immediate response to shift to QA, while genes with products in the remaining 7 metabolic modules generally show a delayed response to shift to QA. The additional QA-responsive cutinase transcription factor-1β (NCU03643) is found to have a delayed response to shift to QA. The series of microarray experiments are used to expand the previously identified genetic network describing the qa gene cluster to include all 50 QA-responsive genes including the second transcription factor (NCU03643). These studies illustrate new methodologies from systems biology to guide model-driven discoveries about a core metabolic network involving carbon and amino acid metabolism in N. crassa.
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spelling pubmed-31148022011-06-21 Systems Biology of the qa Gene Cluster in Neurospora crassa Tang, Xiaojia Dong, Wubei Griffith, James Nilsen, Roger Matthes, Allison Cheng, Kevin B. Reeves, Jaxk Schuttler, H.-Bernd Case, Mary E. Arnold, Jonathan Logan, David A. PLoS One Research Article An ensemble of genetic networks that describe how the model fungal system, Neurospora crassa, utilizes quinic acid (QA) as a sole carbon source has been identified previously. A genetic network for QA metabolism involves the genes, qa-1F and qa-1S, that encode a transcriptional activator and repressor, respectively and structural genes, qa-2, qa-3, qa-4, qa-x, and qa-y. By a series of 4 separate and independent, model-guided, microarray experiments a total of 50 genes are identified as QA-responsive and hypothesized to be under QA-1F control and/or the control of a second QA-responsive transcription factor (NCU03643) both in the fungal binuclear Zn(II)2Cys6 cluster family. QA-1F regulation is not sufficient to explain the quantitative variation in expression profiles of the 50 QA-responsive genes. QA-responsive genes include genes with products in 8 mutually connected metabolic pathways with 7 of them one step removed from the tricarboxylic (TCA) Cycle and with 7 of them one step removed from glycolysis: (1) starch and sucrose metabolism; (2) glycolysis/glucanogenesis; (3) TCA Cycle; (4) butanoate metabolism; (5) pyruvate metabolism; (6) aromatic amino acid and QA metabolism; (7) valine, leucine, and isoleucine degradation; and (8) transport of sugars and amino acids. Gene products both in aromatic amino acid and QA metabolism and transport show an immediate response to shift to QA, while genes with products in the remaining 7 metabolic modules generally show a delayed response to shift to QA. The additional QA-responsive cutinase transcription factor-1β (NCU03643) is found to have a delayed response to shift to QA. The series of microarray experiments are used to expand the previously identified genetic network describing the qa gene cluster to include all 50 QA-responsive genes including the second transcription factor (NCU03643). These studies illustrate new methodologies from systems biology to guide model-driven discoveries about a core metabolic network involving carbon and amino acid metabolism in N. crassa. Public Library of Science 2011-06-14 /pmc/articles/PMC3114802/ /pubmed/21695121 http://dx.doi.org/10.1371/journal.pone.0020671 Text en Tang et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Tang, Xiaojia
Dong, Wubei
Griffith, James
Nilsen, Roger
Matthes, Allison
Cheng, Kevin B.
Reeves, Jaxk
Schuttler, H.-Bernd
Case, Mary E.
Arnold, Jonathan
Logan, David A.
Systems Biology of the qa Gene Cluster in Neurospora crassa
title Systems Biology of the qa Gene Cluster in Neurospora crassa
title_full Systems Biology of the qa Gene Cluster in Neurospora crassa
title_fullStr Systems Biology of the qa Gene Cluster in Neurospora crassa
title_full_unstemmed Systems Biology of the qa Gene Cluster in Neurospora crassa
title_short Systems Biology of the qa Gene Cluster in Neurospora crassa
title_sort systems biology of the qa gene cluster in neurospora crassa
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3114802/
https://www.ncbi.nlm.nih.gov/pubmed/21695121
http://dx.doi.org/10.1371/journal.pone.0020671
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