Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110.

With the goal of solving the whole-cell problem with Escherichia coli K-12 as a model cell, highly accurate genomes were determined for two closely related K-12 strains, MG1655 and W3110. Completion of the W3110 genome and comparison with the MG1655 genome revealed differences at 267 sites, including 251 sites with short, mostly single-nucleotide, insertions or deletions (indels) or base substitutions (totaling 358 nucleotides), in addition to 13 sites with an insertion sequence element or defective prophage in only one strain and two sites for the W3110 inversion. Direct DNA sequencing of PCR products for the 251 regions with short indel and base disparities revealed that only eight sites are true differences. The other 243 discrepancies were due to errors in the original MG1655 sequence, including 79 frameshifts, one amino-acid residue deletion, five amino-acid residue insertions, 73 missense, and 17 silent changes within coding regions. Errors in the original MG1655 sequence (<1 per 13,000 bases) were mostly within portions sequenced with out-dated technology based on radioactive chemistry.

Identification and comparative analysis of the large subunit mitochondrial ribosomal proteins of Neurospora crassa.

The mitochondrial ribosome (mitoribosome) has highly evolved from its putative prokaryotic ancestor and varies considerably from one organism to another. To gain further insights into its structural and evolutionary characteristics, we have purified and identified individual mitochondrial ribosomal proteins of Neurospora crassa by mass spectrometry and compared them with those of the budding yeast Saccharomyces cerevisiae. Most of the mitochondrial ribosomal proteins of the two fungi are well conserved with each other, although the degree of conservation varies to a large extent. One of the N. crassa mitochondrial ribosomal proteins was found to be homologous to yeast Mhr1p that is involved in homologous DNA recombination and genome maintenance in yeast mitochondria.

Proteome analysis of an aerobic hyperthermophilic crenarchaeon, Aeropyrum pernix K1.

We analyzed the proteome of a crenararchaeon, Aeropyrum pernix K1, by using the following four methods: (i) two-dimensional PAGE followed by MALDI-TOF MS, (ii) one-dimensional SDS-PAGE in combination with two-dimensional LC-MS/MS, (iii) multidimensional LC-MS/MS, and (iv) two-dimensional PAGE followed by amino-terminal amino acid sequencing. These methods were found to be complementary to each other, and biases in the data obtained in one method could largely be compensated by the data obtained in the other methods. Consequently a total of 704 proteins were successfully identified, 134 of which were unique to A. pernix K1, and 19 were not described previously in the genomic annotation. We found that the original annotation of the genomic data of this archaeon was not adequate in particular with respect to proteins of 10-20 kDa in size, many of which were described as hypothetical. Furthermore the amino-terminal amino acid sequence analysis indicated that surprisingly the translation of 52% of their genes starts with TTG in contrast to ATG (28%) and GTG (20%). Thus, A. pernix K1 is the first example of an organism in which TTG is the most predominant translational initiation codon.

Systematic characterization of Escherichia coli genes/ORFs affecting biofilm formation.

To understand the nature and function of bacterial biofilm and the process of its formation, we have performed systematic screening of a complete set of Escherichia coli genes/open reading frames (ORFs) to identify those that affect biofilm development upon over-expression. In contrast to the biofilm of strain AG1 used as a control, some of the genes/ORFs when over-expressed led to the formation of an abnormal biofilm such as thin, mat-like, filamentous or one easily detaching from various surfaces. Disruptants of selected genes were constructed in order to clarify their roles in the different stages of biofilm formation. Our results suggest that diverse metabolic pathways contribute to the development of biofilm.

Tag-mediated isolation of yeast mitochondrial ribosome and mass spectrometric identification of its new components.

Mitochondrial ribosomal proteins (mrps) of the budding yeast, Saccharomyces cerevisiae, have been extensively characterized genetically and biochemically. However, the list of the genes encoding individual mrps is still not complete and quite a few of the mrps are only predicted from their similarity to bacterial ribosomal proteins. We have constructed a yeast strain in which one of the small subunit proteins, termed Mrp4, was tagged with S-peptide and used for affinity purification of mitochondrial ribosome. Mass spectrometric analysis of the isolated proteins detected most of the small subunit mrps which were previously identified or predicted and about half of the large subunit mrps. In addition, several proteins of unknown function were identified. To confirm their identity further, we added tags to these proteins and analyzed their localization in subcellular fractions. Thus, we have newly established Ymr158w (MrpS8), Ypl013c (MrpS16), Ymr188c (MrpS17) and Ygr165w (MrpS35) as small subunit mrps and Img1, Img2, Ydr116c (MrpL1), Ynl177c (MrpL22), Ynr022c (MrpL50) and Ypr100w (MrpL51) as large subunit mrps.

Isolation and characterization of Saccharomyces cerevisiae genes differentially expressed under different growth conditions.

The budding yeast Saccharomyces cerevisiae, like many other microorganisms, responds to nutrient starvation by arresting growth and entering into a non-proliferating stationary phase. Studies on the response of S. cerevisiae cells to growth arrest might provide further insight into the non-proliferative states of cells in multi-cellular eukaryotic organisms. Changes might occur at the transcription, translation, and post-translational levels in cells upon entry into the stationary phase. To search for the genes differentially expressed in yeast cells during different growth phases, we have performed systematic Northern hybridization experiments using probes prepared for a large number of genes/ORFs. We have thus isolated and characterized 42 cDNA clones containing genes hyper-expressed in the post-diauxic phase. Some of them have already been characterized, and many others show similarity to known yeast genes or genes of other organisms. However, eleven of them were found to be unrelated to any known genes. We have characterized some of these genes as described below. Also, a possible cis-element for transcriptional regulation was identified.