Progress in Arabidopsis genome sequencing and functional genomics.

Arabidopsis thaliana has a relatively small genome of approximately 130 Mb containing about 10% repetitive DNA. Genome sequencing studies reveal a gene-rich genome, predicted to contain approximately 25000 genes spaced on average every 4.5 kb. Between 10 to 20% of the predicted genes occur as clusters of related genes, indicating that local sequence duplication and subsequent divergence generates a significant proportion of gene families. In addition to gene families, repetitive sequences comprise individual and small clusters of two to three retroelements and other classes of smaller repeats. The clustering of highly repetitive elements is a striking feature of the A. thaliana genome emerging from sequence and other analyses.

Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.

The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins.

Misfolding of chloramphenicol acetyltransferase due to carboxy-terminal truncation can be corrected by second-site mutations.

Folding of chloramphenicol acetyltransferase (CAT) in Escherichia coli is hampered by deletion of the carboxy-terminal tail including the last residue of the carboxy-terminal alpha-helix. Such truncated CAT polypeptides quantitatively aggregate into cytoplasmic inclusion bodies, which results in absence of a chloramphenicol-resistant phenotype for the producing host. In this paper, a genetic approach is presented to examine this aggregation process in more detail. Random mutagenesis of inactive CAT followed by direct phenotypic selection for revertants with restored chloramphenicol resistance was used to isolate second-site suppressors of inactive truncation mutants of CAT. Two random mutagenesis procedures, independently of each other, yielded a unique substitution of Phe for Leu at amino acid position 145. This second-site mutation does not drastically affect the proteins' stability under normal growth conditions of E. coli. Hence, the introduction of Phe at amino acid position 145 improves the ability of the protein to fold into a soluble, enzymatically active conformation. The conservative character of the Leu145Phe replacement indicates that limited changes at crucial positions can have important effects on protein folding in vivo.

Identification of local carboxy-terminal hydrophobic interactions essential for folding or stability of chloramphenicol acetyltransferase.

The role of the carboxy terminal in folding and stabilization of type I chloramphenicol acetyltransferase (CAT1) has been studied by mutagenesis and Fourier transform infrared analysis. We have shown that a CAT mutant truncated by seven amino acid residues folds into active protein. In this study, the last three residues of this truncated CAT mutant were randomized to detect structural information required for achieving a native enzyme conformation. Statistical analysis of sequencing data from randomly chosen mutants revealed that the amino-terminal CAT fragment of 212 amino acid residues is the shortest deletion mutant able to adopt a soluble, enzymatically active structure. This minimal length corresponds to a protein with full-length alpha5-helix in the three-dimensional crystal structure of CAT type III. The amino acid preferences at the carboxy terminal in the randomization experiments suggest that this helix also forms completely in the shortened CAT mutants. In addition correct folding and/or stabilization requires the formation of a hydrophobic + microdomain at the end of the alpha5-helix. The role of this hydrophobic interaction in CAT folding and structure stabilization is discussed.

Insertional re-activation of a chloramphenicol acetyltransferase misfolding mutant protein.

The deletion of nine residues from the C-terminus of the bacterial chloramphenicol acetyltransferase (CAT) results in deposition of the mutant protein in cytoplasmic inclusion bodies and loss of chloramphenicol resistance in Escherichia coli. This folding defect is relieved by C-terminal fusion of the polypeptide with as few as two residues. Based on these observations, efficient positive selection for the cloning of DNA fragments has been demonstrated. The cloning vector encodes a C-terminally truncated CAT protein. Restriction sites in front of the stop codon allow the insertion of target DNA, resulting in the production of properly folded CAT fusion proteins and regained chloramphenicol resistance. The positive selection of recombinants is accomplished by growth of transformants on chloramphenicol-containing agar plates. The method appears particularly convenient for the cloning of DNA fragments amplified by the PCR because minimal information to restore CAT folding can be included in the primers. The cloning of random sequences shows that the folding defect can be relieved by fusion to a wide variety of peptides, providing great flexibility to the positive selection system. This vector may also contribute to the determination of the role of the C-terminus in CAT folding.

Carboxyl terminus is essential for intracellular folding of chloramphenicol acetyltransferase.

Chloramphenicol acetyltransferase (CAT, EC 2.3.1.28) is a bacterial chloramphenicol resistance marker that is commonly used as a reporter enzyme in gene expression studies and as a carrier protein for the production of fused peptides. The latter can be done by insertion of target sequences into the native ScaI site near the 3'-end of the Tn9 cat gene. CAT activity in the resulting fusion proteins is retained. We observed that creation of a stop codon at this ScaI, which causes a COOH-terminal 9-amino acid deletion, results in loss of chloramphenicol resistance and total deposition of the mutant protein in inclusion bodies in Escherichia coli. Cytoplasmic solubility and enzyme activity are completely regained by elongation of this mutant with only 2 residues. Apparently, terminal residues of the alpha 5-helix play a crucial role in achieving the native conformation of nascent CAT molecules. Thus, CAT provides an interesting model system for mutational analysis of protein folding in vivo.