Enhanced acetohydroxy acid synthase III activity in an ilvH mutant of Escherichia coli K-12

Identification of Cyclic-di-GMP-Modulating Protein Residues by Bidirectionally Evolving a Social Behavior in Pseudomonas fluorescens

Modulation of the intracellular cyclic di-GMP (c-di-GMP) pool is central to the formation of structured bacterial communities. Genome annotations predict the presence of dozens of conserved c-di-GMP catalytic enzymes in many bacterial species, but the functionality and regulatory control of the vast majority remain underexplored. Here, we begin to fill this gap by utilizing an experimental evolution system in Pseudomonas fluorescens Pf0-1, which repeatedly produces a unique social behavior through bidirectional transitions between two distinct phenotypes converging on c-di-GMP modulation. Parallel evolution of 33 lineages captured 147 unique mutations among 191 evolved isolates in genes that are empirically demonstrated, bioinformatically predicted, or previously unknown to impact the intracellular pool of c-di-GMP. Quantitative chemistry confirmed that each mutation causing the phenotypic shift either amplifies or reduces c-di-GMP production. We identify missense or in-frame deletion mutations in numerous diguanylate cyclase genes that largely fall outside the conserved catalytic domain. We also describe a novel relationship between a regulatory component of branched-chain amino acid biosynthesis and c-di-GMP production, and predict functions of several other unexpected proteins that clearly impact c-di-GMP production. Sequential mutations that continuously disrupt or recover c-di-GMP production across discrete functional elements suggest a complex and underappreciated interconnectivity within the c-di-GMP regulome of P. fluorescens. IMPORTANCE Microbial communities comprise densely packed cells where competition for space and resources is fierce. Aging colonies of Pseudomonas fluorescens are known to repeatedly produce mutants with two distinct phenotypes that physically work together to spread away from the overcrowded population. We demonstrate that the mutants with one phenotype produce high levels of cyclic di-GMP (c-di-GMP) and those with the second phenotype produce low levels. C-di-GMP is an intracellular signaling molecule which regulates many bacterial traits that cause tremendous clinical and environmental problems. Here, we analyze 147 experimentally selected mutations, which manifest either of the two phenotypes, to identify key residues in diverse proteins that force or shut down c-di-GMP production. Our data indicate that the intracellular pool of c-di-GMP is modulated through the catalytic activities of many independent c-di-GMP enzymes, which appear to be in tune with several proteins with no known links to c-di-GMP modulation.

Fermentative production of branched chain amino acids: a focus on metabolic engineering

The branched chain amino acids (BCAAs), L-valine, L-leucine, and L-isoleucine, have recently been attracting much attention as their potential to be applied in various fields, including animal feed additive, cosmetics, and pharmaceuticals, increased. Strategies for developing microbial strains efficiently producing BCAAs are now in transition toward systems metabolic engineering from random mutagenesis. The metabolism and regulatory circuits of BCAA biosynthesis need to be thoroughly understood for designing system-wide metabolic engineering strategies. Here we review the current knowledge on BCAAs including their biosynthetic pathways, regulations, and export and transport systems. Recent advances in the development of BCAA production strains are also reviewed with a particular focus on L-valine production strain. At the end, the general strategies for developing BCAA overproducers by systems metabolic engineering are suggested.

Genes of non-typeable Haemophilus influenzae expressed during interaction with human epithelial cell lines

Non-typeable Haemophilus influenzae may infect the lower respiratory airways of chronic obstructive pulmonary disease patients. We characterized genes of non-typeable H. influenzae expressed during interaction with two human respiratory tract-derived epithelial cell lines. A library of 8000 clones was constructed in H. influenzae Rd (rec1) by cloning chromosomal fragments upstream of a promoterless cat gene. Exposure of this library to NCI-H292 epithelial cell layers in the presence of chloramphenicol (Cam) resulted in survival of bacteria expressing cat. A total of 52 clones were selected that were resistant to Cam in the presence of epithelial cells of cell line NCI-H292. These did not (n = 42) or hardly grow (n = 10) on sBHI plates containing Cam and were sensitive to Cam in cell culture medium alone. All clones, moreover, survived Cam in the presence of Hep2 epithelial cell layers. Sequence analysis showed that four clones contained sequences without homology to Rd or any other sequence, and therefore contained promoters and parts of open reading frames (ORFs) of novel genes. The other 48 clones were homologous to Rd, and characterization was based upon this genome. Six different functional classes were distinguished: (i) metabolic processes; (ii) stress response; (iii) gene expression; (iv) cell envelope biosynthesis; (v) DNA-related processes and cell division; and (vi) ORFs encoding proteins of unknown function. The contribution of identified genes to non-typeable H. influenzae adaptation to the epithelial cell environment is discussed.

Expression, purification, characterization, and reconstitution of the large and small subunits of yeast acetohydroxyacid synthase

Acetohydroxyacid synthase (AHAS, EC 4.1.3.18) catalyzes the first step in the biosynthesis of the branched-chain amino acids. In bacteria, the enzyme has a large subunit containing the catalytic machinery and a small subunit with a regulatory role. In eucaryotes, the evidence for a regulatory subunit is largely indirect and circumstantial. We investigated the possibility that the yeast open reading frame YCL009c is an AHAS small subunit. Analysis of the DNA sequence shows that it contains all the appropriate transcription, translation and regulatory signals. YCL009c was shown to be expressed in yeast and the protein localized in mitochondria where it undergoes removal of a transit peptide targeting sequence. This putative small subunit protein (ilv6) and the catalytic subunit of yeast AHAS (ilv2) were each overexpressed in Escherichia coli and purified to near homogeneity. Reconstitution studies showed that the ilv6 protein stimulates the catalytic activity of the ilv2 protein by up to 7-fold (from 6.8 +/- 0.7 to 49.0 +/- 1.8 U/mg) and confers upon it sensitivity to inhibition by valine (Ki = 0.16 +/- 0.02 mM). Valine inhibition is partially reversed by ATP. The reconstitution is favored by high concentrations of potassium phosphate ( approximately 1 M) and at neutral pH. Under optimal conditions for reconstitution, a dissociation constant for the subunits of 70 +/- 7 nM was determined. Valine inhibition is partial, resulting in a specific activity that is similar to that of the ilv2 protein alone. However, measurements of the Km for substrate rule out the possibility that valine inhibition is accomplished by dissociation of the subunits.

Purification and characterization of the oxygen-sensitive acetohydroxy acid synthase from the archaebacterium Methanococcus aeolicus

Acetohydroxy acid synthase (EC 4.1.3.18) of the archaebacterium Methanococcus aeolicus was purified 1,150-fold to homogeneity. The molecular weight of the purified enzyme was 125,000, and it contained only one type of subunit (M(r) = 58,000). The amino-terminal sequence had 46 to 57% similarity to those of the large subunits of the eubacterial anabolic enzymes and 37 to 43% similarity to those of the yeast and plant enzymes. The methanococcal enzyme had a pH optimum of 7.6. The pI, estimated by chromatofocusing, was 5.6. Activity required Mg2+ or Mn2+ ions, thiamine pyrophosphate, and a flavin. Flavin adenine dinucleotide, flavin mononucleotide, and riboflavin plus 10 mM phosphate all supported activity. However, activity was strongly inhibited by these flavins at 0.3 mM. The Michaelis constants for pyruvate, MgCl2, MnCl2, thiamine pyrophosphate, flavin adenine dinucleotide, and flavin mononucleotide were 6.8 mM, 0.3 mM, 0.16 mM, 1.6 microM, 0.4 microM, and 1.3 microM, respectively. In cell extracts, the enzyme was sensitive to O2 (half-life = 2.7 min with 5% O2 in the headspace), but the purified enzyme was less sensitive to O2 (half-life = 78.0 min with 20% O2). Reconstitution of the enzyme with flavin adenine dinucleotide increased the sensitivity to O2. Moreover, in the assay the homogeneous enzyme was rapidly inactivated by O2, and the concentration required for 50% inhibition (I50) was obtained with an atmosphere of 0.11% O2. The methanococcal enzyme has similarities to the eubacterial and eucaryotic enzymes, consistent with the ancient origin of the archaebacterial enzyme.

Functions of the gene products of Escherichia coli

A list of currently identified gene products of Escherichia coli is given, together with a bibliography that provides pointers to the literature on each gene product. A scheme to categorize cellular functions is used to classify the gene products of E. coli so far identified. A count shows that the numbers of genes concerned with small-molecule metabolism are on the same order as the numbers concerned with macromolecule biosynthesis and degradation. One large category is the category of tRNAs and their synthetases. Another is the category of transport elements. The categories of cell structure and cellular processes other than metabolism are smaller. Other subjects discussed are the occurrence in the E. coli genome of redundant pairs and groups of genes of identical or closely similar function, as well as variation in the degree of density of genetic information in different parts of the genome.