To estimate the minimal gene set required to sustain bacterial life in nutritious conditions, we carried out a systematic inactivation of Bacillus subtilis genes. Among Ϸ4,100 genes of the organism, only 192 were shown to be indispensable by this or previous work. Another 79 genes were predicted to be essential. The vast majority of essential genes were categorized in relatively few domains of cell metabolism, with about half involved in information processing, one-fifth involved in the synthesis of cell envelope and the determination of cell shape and division, and one-tenth related to cell energetics. Only 4% of essential genes encode unknown functions. Most essential genes are present throughout a wide range of Bacteria, and almost 70% can also be found in Archaea and Eucarya. However, essential genes related to cell envelope, shape, division, and respiration tend to be lost from bacteria with small genomes. Unexpectedly, most genes involved in the Embden-Meyerhof-Parnas pathway are essential. Identification of unknown and unexpected essential genes opens research avenues to better understanding of processes that sustain bacterial life.

No abstract

from random initial angles (involving both protein and RNA), and stem loops DIS-2, SL-C and SL-D were refined independently using dipolar couplings obtained for the isolated stem loops. This approach is valid because the NMR chemical shifts and NOE cross peak patterns and intensities of the isolated stem loops and those in the NC-mW CES complex were indistinguishable 15 . Statistical information and superposition images are provided in Supplementary Table S1 and Fig. S5, respectively. Structure figures were generated with PyMOL (http://pymol.sourceforge.net).

No abstract

No abstract

with the analysis of folding of specific endogenous proteins in mutant strains, these studies have led to signifi-Hermann Herder Str. 7 D-79104 Freiburg cant advances in our understanding of protein folding in the complex cellular milieu. Germany † Department of Biomolecular Chemistry The Welcoming Committee for Nascent Polypeptide Chains University of Wisconsin 1300 University Avenue Nascent chains emerging at the peptide exit tunnel of Madison, Wisconsin 53706 the ribosome are awaited by a welcoming committee of ribosome-associated chaperones. These factors have been most thoroughly studied in E. coli. Trigger factor (TF), which is found in all eubacteria analyzed, is the Cellular synthesis of polypeptides is an amazing, commajor protein that cross-links to virtually all nascent plex, and efficient process. An E. coli cell utilizes up to chains of secretory and cytosolic proteins tested (Valent 20,000 ribosomes to produce an estimated total of et al., 1995; Hesterkamp et al., 1996). It may be posi-30,000 polypeptides per minute. Yet it is only the begintioned close to the exit site, as it cross-links to ribosomening. Each newly made protein must be folded into its associated chains 57 residues in length. TF, which has a correct tertiary structure. How this is achieved is one of central domain with homology to FK506 binding proteins the most basic, and complicated, questions of molecular (FKBPs), displays peptidyl-prolyl-cis-trans isomerase biology. and chaperone-like activities in vitro. It is unclear which When does the process of folding begin in the lifetime of these activities is required for its function in vivo. of a protein? Crystallographic data of bacterial ribo-Recent genetic studies provide clues suggesting a somes identified a peptide exit tunnel in the large subunit role of TF in protein folding in vivo. ⌬tig mutants lacking with a length of 100 Å and an average diameter of about TF have no apparent phenotype and no major defects 20 Å (Ban et al., 1999). This tunnel is long enough to in folding of newly synthesized proteins (Deuerling et accommodate extended chains of about 30 residues al., 1999; Teter et al., 1999). However, in the absence of and perhaps longer peptides in helical conformation, the Hsp70 chaperone DnaK, ⌬tig mutants are inviable. but certainly not peptides with tertiary structure. Once Upon depletion of DnaK in ⌬tig strains, more than 40 the N-terminal residues are synthesized, the nascent different newly synthesized cytosolic proteins aggrepolypeptide emerges into the crowded environment of gate, indicating a role for TF in folding of cytosolic prothe cytosol. It is well established that nascent proteins teins in cooperation with the DnaK chaperone system can fold cotranslationally (i.e., while still attached to (see below). ribosomes) in cell-free translation systems. Recently, TF binds in vitro with 1:1 stoichiometry to the large a study using the Semliki Forest virus capsid protein subunits of both translating and nontranslating riboestablished that cotranslational folding can...

In addition to assisting with protein folding, SSB and NAC also regulate ribosome biogenesis (see also companion paper from Albanèse et al. in this issue).

No abstract