Regulation of branched-chain amino acid biosynthesis in Neurospora crassa: cloning and characterization of the leu-1 and ilv-3 genes

Branched-chain amino acid biosynthesis in fungi

Branched-chain amino acids (BCAAs)-isoleucine, leucine, and valine-are synthesized by fungi. These amino acids are important components of proteins and secondary metabolites. The biochemical pathway for BCAA biosynthesis is well-characterized in the yeast Saccharomyces cerevisiae. The biosynthesis of these three amino acids is interconnected. Different precursors are metabolized in multiple steps through shared enzymes to produce isoleucine and valine, and the valine biosynthesis pathway branches before the penultimate step to a series of leucine biosynthesis-specific steps to produce leucine. Recent efforts have made advances toward characterization of the BCAA biosynthesis pathway in several fungi, revealing diversity in gene duplication and functional divergence in the genes for these enzymatic steps in different fungi. The BCAA biosynthesis pathway is regulated by the transcription factor LEU3 in S. cerevisiae, and LeuB in Aspergillus nidulans and Aspergillus fumigatus, and the activity of these transcription factors is modulated by the leucine biosynthesis pathway intermediate α-isopropylmalate. Herein, we discuss recent advances in our understanding of the BCAA pathway and its regulation, focusing on filamentous ascomycete fungi and comparison with the well-established process in yeast.

A Sordaria macrospora mutant lacking the leu1 gene shows a developmental arrest during fruiting body formation

Developmental mutants with defects in fruiting body formation are excellent resources for the identification of genetic components that control cellular differentiation processes in filamentous fungi. The mutant pro4 of the ascomycete Sordaria macrospora is characterized by a developmental arrest during the sexual life cycle. This mutant generates only pre-fruiting bodies (protoperithecia), and is unable to form ascospores. Besides being sterile, pro4 is auxotrophic for leucine. Ascospore analysis revealed that the two phenotypes are genetically linked. After isolation of the wild-type leu1 gene from S. macrospora, complementation experiments demonstrated that the gene was able to restore both prototrophy and fertility in pro4. To investigate the control of leu1 expression, other genes involved in leucine biosynthesis specifically and in the general control of amino acid biosynthesis ("cross-pathway control") have been analysed using Northern hybridization and quantitative RT-PCR. These analyses demonstrated that genes of leucine biosynthesis are transcribed at higher levels under conditions of amino acid starvation. In addition, the expression data for the cpc1 and cpc2 genes indicate that cross-pathway control is superimposed on leucine-specific regulation of fruiting body development in the leu1 mutant. This was further substantiated by growth experiments in which the wild-type strain was found to show a sterile phenotype when grown on a medium containing the amino acid analogue 5-methyl-tryptophan. Taken together, these data show that pro4 represents a novel mutant type in S. macrospora, in which amino acid starvation acts as a signal that interrupts the development of the fruiting body.

Regulation of yeast acetohydroxyacid synthase by valine and ATP

The first step in the common pathway for the biosynthesis of branched-chain amino acids is catalysed by acetohydroxyacid synthase (AHAS; EC 4.1.3.18). The enzyme is found in plants, fungi and bacteria, and is regulated by controls on transcription and translation, and by allosteric modulation of catalytic activity. It has long been known that the bacterial enzyme is composed of two types of subunit, and a similar arrangement has been found recently for the yeast and plant enzymes. One type of subunit contains the catalytic machinery, whereas the other has a regulatory function. Previously, we have shown [Pang and Duggleby (1999) Biochemistry 38, 5222--5231] that yeast AHAS can be reconstituted from its separately purified subunits. The reconstituted enzyme is inhibited by valine, and ATP reverses this inhibition. In the present work, we further characterize the structure and the regulatory properties of reconstituted yeast AHAS. High phosphate concentrations are required for reconstitution and it is shown that these conditions are necessary for physical association between the catalytic and regulatory subunits. It is demonstrated by CD spectral changes that ATP binds to the regulatory subunit alone, most probably as MgATP. Neither valine nor MgATP causes dissociation of the regulatory subunit from the catalytic subunit. The specificity of valine inhibition and MgATP activation are examined and it is found that the only effective analogue of either regulator of those tested is the non-hydrolysable ATP mimic, adenosine 5'-[beta,gamma-imido]triphosphate. The kinetics of regulation are studied in detail and it is shown that the activation by MgATP depends on the valine concentration in a complex manner that is consistent with a proposed quantitative model.

Cloning of the dihydroxyacid dehydratase-encoding gene (ILV3) from Saccharomyces cerevisiae

The biosynthesis of branched-chain amino acids (aa) involves three shared pathways through which pyruvate or alpha-ketobutyrate are converted into alpha-keto acids, precursors of valine, leucine or isoleucine. In eukaryotes, few of these common enzymes have been purified to homogeneity, and the whole complement of biosynthetic genes has not been cloned from a single species. In yeasts, most of these genes (ILV genes) have been cloned and sequenced, with the exception of that coding for dihydroxyacid dehydratase (DAD, EC 4.2.1.9), the third enzyme in the common pathways. We have isolated Saccharomyces cerevisiae genomic sequences by hybridization to an oligodeoxyribonucleotide (oligo) probe designed from a highly conserved domain among bacterial DAD-encoding genes. The cloned sequences have been located to S. cerevisiae chromosome X, mapped within 0.4 centiMorgans (cM) of the ilv3 locus, and found to complement the ilv3 mutations of various yeast strains. Nucleotide (nt) and aa sequence analyses of the longest open reading frame (ORF) located within the cloned sequences identified them as the ILV3 gene, which codes for the yeast DAD. With our cloning of ILV3, yeast becomes the only eukaryotic system from which all ILV genes have been cloned, thus allowing direct molecular analyses of their regulation.

The leu-1 gene of Neurospora crassa: nucleotide and deduced amino acid sequence comparisons

The Neurospora crassa leu-1 gene encodes beta-isopropylmalate dehydrogenase (IPMDH; EC 1.1.1.85), an enzyme in the leucine biosynthetic pathway. We determined the nucleotide sequence of the entire leu-1 gene and of four independent cDNA clones. By comparing the genomic and cDNA sequences, four introns were identified in the 5' portion of the gene and a single open reading frame was established. One of the introns is located within the 5'-noncoding region of the transcript. The deduced amino acid sequence encoded by leu-1 was aligned with that of the homologous yeast enzyme and extensive sequence identity was uncovered. The lesion present in a conventional leu-1 mutant was identified as the insertion of a single base pair.