The Inducible Quinate-Shikimate Catabolic Pathway in Neurospora crassa: Genetic Organization

Chaleff, R. S.

doi:10.1099/00221287-81-2-337

Cited by 34 publications

(15 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, at least two distinct forms of each enzyme have arisen by convergent evolution. Fungi such as Neurospora crassa and Aspergillus nidulans , and the Gram‐positive bacterium Corynebacterium glutamicum , use cytosolic quinate pathway enzymes which include an NAD + ‐dependent Q/SDH and a ‘type II’ DHQ (Chaleff, 1974a, b; Hawkins et al ., ; Hawkins et al ., ; Teramoto et al ., ). In contrast, the genus Acinetobacter , which has represented a model for quinate degradation among Gram‐negative bacteria, employs structurally unrelated membrane‐associated enzymes to catalyze the equivalent reactions (Elsemore and Ornston, ; Elsemore and Ornston, ; van Kleef and Duine, ).…”

Section: Introductionmentioning

confidence: 99%

Structurally diverse dehydroshikimate dehydratase variants participate in microbial quinate catabolism

Peek

Roman

Moran

et al. 2016

Molecular Microbiology

View full text Add to dashboard Cite

Quinate and shikimate can be degraded by a number of microbes. Dehydroshikimate dehydratases (DSDs) play a central role in this process, catalyzing the conversion of 3-dehydroshikimate to protocatechuate, a common intermediate of aromatic degradation pathways. DSDs have applications in metabolic engineering for the production of valuable protocatechuate-derived molecules. Although a number of Gram-negative bacteria are known to catabolize quinate and shikimate, only limited information exists on the quinate/shikimate catabolic enzymes found in these organisms. Here, we have functionally and structurally characterized a putative DSD designated QuiC1, which is present in some pseudomonads. The QuiC1 protein is not related by sequence with previously identified DSDs from the Gram-negative genus, Acinetobacter, but instead shows limited sequence identity in its N-terminal half with fungal DSDs. Analysis of a Pseudomonas aeruginosa quiC1 gene knock-out demonstrates that it is important for growth on either quinate or shikimate. The structure of a QuiC1 enzyme from P. putida reveals that the protein is a fusion of two distinct modules: an N-terminal sugar phosphate isomerase-like domain associated with DSD activity and a novel C-terminal hydroxyphenylpyruvate dioxygenase-like domain. The results of this study highlight the considerable diversity of enzymes that participate in quinate/shikimate catabolism in different microbes.

show abstract

Section: Introductionmentioning

confidence: 99%

Structurally diverse dehydroshikimate dehydratase variants participate in microbial quinate catabolism

Peek

Roman

Moran

et al. 2016

Molecular Microbiology

View full text Add to dashboard Cite

show abstract

“…During the catabolism of uric acid to ammonia, the three initial enzymes are repressed by ammonia, whereas the last two enzymes are constitutively synthesized. Interestingly, uric acid, which is an intermediate in the pathway, induces uricase and allantoicase, whereas allantoinase is induced by uric acid and allantoin (402,403). N. crassa PCO-1 (TR_35454, TA_172139, and TV_54183) regulates the expression of several genes encoding enzymes required for the catabolism of purines (404).…”

Section: Nitrogen Metabolismmentioning

confidence: 99%

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

Schmoll

Dattenböck

Carreras-Villaseñor

et al. 2016

Microbiol Mol Biol Rev

163

195

View full text Add to dashboard Cite

SUMMARYThe genusTrichodermacontains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for “hot topic” research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism inT. reesei,T. atroviride, andT. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of eachTrichodermaspecies discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved inN-linked glycosylation was detected, as were indications for the ability ofTrichodermaspp. to generate hybrid galactose-containingN-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique toTrichoderma, and these warrant further investigation. We found interesting expansions in theTrichodermagenus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique toT. atrovirideis the duplication of the alternative sulfur amino acid synthesis pathway.

show abstract

“…Establishment of liquid cultures follows [35]–[36]. A culture in a 250 ml flask with 50 ml of Fries medium [29] + sucrose (1.5%) + agar (1.5%) is inoculated, grown for 2 days at 30°C and then is shifted to room temperature under light for 5–6 days to induce conidiation.…”

Section: Methodsmentioning

confidence: 99%

Systems Biology of the qa Gene Cluster in Neurospora crassa

et al. 2011

View full text Add to dashboard Cite

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.

show abstract

The Inducible Quinate-Shikimate Catabolic Pathway in Neurospora crassa: Genetic Organization

Cited by 34 publications

References 17 publications

Structurally diverse dehydroshikimate dehydratase variants participate in microbial quinate catabolism

Structurally diverse dehydroshikimate dehydratase variants participate in microbial quinate catabolism

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

Systems Biology of the qa Gene Cluster in Neurospora crassa

Contact Info

Product

Resources

About