title: Setting up standards and a reference map for the alkaline proteome of the Gram-positive bacterium Lactococcus lactis.
abstract: Despite the fact that almost 39% of the theoretical expressed proteins of Lactococcus lactis have a predicted isoelectric point above 7, these proteins have not been studied in previous proteome analyses. In the present study, we set up a reference map of alkaline lactococcal proteins by using immobilized pH gradients (IPG) spanning pH 6 to 12 and 9 to 12, and protein identification by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). Different electrophoresis systems for isoelectric focusing were evaluated to optimize the first dimension. Best results were obtained by sample application using cup-loading at the anodic side and increasing the final voltage up to 8000 V for IPGs, using N,N-dimethylacrylamide as monomer. After two-dimensional gel electrophoresis of extracts obtained from exponentially growing cells, about 200 protein spots were selected for identification by peptide mass fingerprinting. With MALDI-TOF MS, 153 proteins were identified that were the products of 85 different genes. Their predicted isoelectric points range from as high as 11.31 to as low as 6.34. Ribosomal proteins, hypothetical proteins and proteins with unknown function represent the largest groups of identified proteins. For further classification, the codon adaptation index (CAI) and grand average of hydropathicity (GRAVY) for each lactococcal protein were calculated. The protein with the lowest CAI identified in this study is the manganese ABC transporter ATP-binding protein. Less than 10% of the alkaline lactococcal proteins have a smaller CAI. The highest GRAVY for an identified protein is 0.26. The complete in silico data of Lactococcus lactis as well as clickable reference maps are available at www.wzw.tum.de/proteomik/lactis.
authors.affiliation: FG Proteomik, Technische Universität München, Munich, Germany.
authors.forename: Oliver
authors.initials: O
authors.lastname: Drews
authors.forename: Gerold
authors.initials: G
authors.lastname: Reil
authors.forename: Harun
authors.initials: H
authors.lastname: Parlar
authors.forename: Angelika
authors.initials: A
authors.lastname: Görg
mesh_terms: D001426:Bacterial Proteins / Q000032:analysis* / Q000737:chemistry / Q000302:isolation & purification / Q000592:standards*; D015180:Electrophoresis, Gel, Two-Dimensional; D006094:Gram-Positive Bacteria / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D057927:Hydrophobic and Hydrophilic Interactions; D007525:Isoelectric Focusing; D007526:Isoelectric Point; D007780:Lacticaseibacillus casei / Q000737:chemistry*; D013058:Mass Spectrometry; D008970:Molecular Weight; D010449:Peptide Mapping / Q000379:methods; D020543:Proteome / Q000592:standards*; D012015:Reference Standards; D012269:Ribosomal Proteins; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D001426:Bacterial Proteins; D020543:Proteome; D012269:Ribosomal Proteins