Cover Picture: Proteomics 20/2008

Abstract

AbstractIn this issue of Proteomics you will find the following highlighted articles:Comprehensively confirmed annotation of short ORFsDuring the California gold rush, prospectors did not look only for large nuggets to pave their road to riches – they also collected gold dust. The proteomic equivalent of dust is the small ORF. It does not pay to put a lower limit on dust or ORF size because almost any size may be turned into “cash” or an important peptide. Wei et al. demonstrate how a combination of conventional genomics and proteomics can find small expressed ORFs in noisy mixtures. Their test system is Shigella flexneri rRNA genes. First, cells were lysed, pre‐fractionated through 100 kDa and 10 kDa cutoff membranes and split into two aliquots, one treated with trypsin the other not. Both were analyzed by LC‐MS/MS and queried for ORFs >15 amino acids. Total labeled RNA probed a DNA array, and, after BLAST classification, revealed 36 new small proteins.Wei, C. et al., Proteomics 2008, 8, 4209–4213.The end of an era: Late stage proteome of cheese bacteriumThe bacterium Streptococcus thermophilus is a common ingredient in food, serving as a starter culture for a wide variety of dairy foods, yogurt in partic­ular, in co‐culture with Lactobacillus delbrueckii ssp. bulgaricus. It is closely related to several pathogenic species but lacks critical genes for pathogenicity. Instead, it is better optimized for lactose digestion than even a teen‐aged boy. Specific genes transport lactose into the cell where it is cleaved by a β‐galactosidase. Because milk is poor in amino acids, some strains of S. thermophilius bring their own protease to digest milk peptides and proteins. This work by Herve‐Jimenez et al. finds that in the latest stage of fermentation a number of critical changes occur: carbon sources are diversified, nitrogen uptake and biosynthesis increase, and there is a dramatic up‐regulation of the entire sulfur‐containing amino acid synthetic pathways. Stimulation by L. bulgaricus is a more complex effect.Herve‐Jimenez, L. et al., Proteomics 2008, 8, 4273–4286.2000‐spot 2‐D DIGE gels yield interesting new CJD marker from CSFCreutzfeld‐Jakob disease (CJD) is a rare, fatal neurodegenerative disease, caused by prions. It is normally seen in either a sporadic (sCJD) or variant (vCJD) form. Differential diagnosis is difficult because the few tests available are weak in sensitivity or specificity, or have not been thoroughly validated. Brechlin et al. report here a much improved cerebrospinal fluid test based on 2‐D DIGE technology and improved sample preparation. Samples were concentrated 20‐fold, then depleted of serum albumin and immunoglobulins, and, finally, labeled with CyDyes. When separated on 24‐cm pH 4 – 7 IPG strips, then on 10 % PAGE‐SDS second dimension gels, >2000 spots could be resolved. After spot analysis for significant differences (volume, p‐value, variance) five spots remained and 4 of the 5 were identified by MALDI‐TOF‐MS. The unidentified spot showed the highest discrimination (p <0.001). Identification work for the fifth spot is continuing.Brechlin, P. et al., Proteomics 2008, 8, 4357–4366.