Essential Biological Processes (essential + biological_process)

Distribution by Scientific Domains


Selected Abstracts


Subcellular localization of proteins labeled with GFP in Xanthomonas citri ssp. citri: targeting the division septum

FEMS MICROBIOLOGY LETTERS, Issue 1 2010
Paula M.M. Martins
Abstract Xanthomonas citri ssp. citri (Xac) is the causal agent of citrus canker, an economically important disease that affects citrus worldwide. To initiate the characterization of essential biological processes of Xac, we constructed integrative plasmids for the ectopic expression of green fluorescent protein (GFP)-labeled proteins within this bacterium. Here, we show that the disruption of the ,-amylase gene (amy), the site of plasmid integration into the bacterial chromosome, does not alter its pathogenesis while abolishing completely the ability of Xac to degrade starch. Furthermore, our GFP expression system was used to characterize ORF XAC3408, a hypothetical protein encoded by Xac that shares significant homology to the FtsZ-stabilizing factor ZapA from Bacillus subtilis (ZapABsu). GFP-XAC3408 expressed in Xac exhibited a septal localization pattern typical of GFP-ZapABsu, which indicates that XAC3408 is the Xac orthologue of the cell division protein ZapABsu. The results demonstrate the potential of GFP labeling for protein functional characterizations in Xac, and, in addition, the Xac mutant strain labeled at the septum constitutes a biological model for the exploration of antibacterial compounds able to inhibit cell division in this plant pathogen. [source]


N-Ace: Using solvent accessibility and physicochemical properties to identify protein N-acetylation sites

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2010
Tzong-Yi Lee
Abstract Protein acetylation, which is catalyzed by acetyltransferases, is a type of post-translational modification and crucial to numerous essential biological processes, including transcriptional regulation, apoptosis, and cytokine signaling. As the experimental identification of protein acetylation sites is time consuming and laboratory intensive, several computational approaches have been developed for identifying the candidates of experimental validation. In this work, solvent accessibility and the physicochemical properties of proteins are utilized to identify acetylated alanine, glycine, lysine, methionine, serine, and threonine. A two-stage support vector machine was applied to learn the computational models with combinations of amino acid sequences, and the accessible surface area and physicochemical properties of proteins. The predictive accuracy thus achieved is 5% to 14% higher than that of models trained using only amino acid sequences. Additionally, the substrate specificity of the acetylated site was investigated in detail with reference to the subcellular colocalization of acetyltransferases and acetylated proteins. The proposed method, N-Ace, is evaluated using independent test sets in various acetylated residues and predictive accuracies of 90% were achieved, indicating that the performance of N-Ace is comparable with that of other acetylation prediction methods. N-Ace not only provides a user-friendly input/output interface but also is a creative method for predicting protein acetylation sites. This novel analytical resource is now freely available at http://N-Ace.mbc.NCTU.edu.tw/. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source]


Determinants of specificity in coagulation proteases

JOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 11 2005
M. J. PAGE
Summary., Proteases play diverse roles in a variety of essential biological processes, both as non-specific catalysts of protein degradation and as highly specific agents that control physiologic events. Here, we review the mechanisms of substrate specificity employed by serine proteases and focus our discussion on coagulation proteases. We dissect the interplay between active site and exosite specificity and how substrate recognition is regulated allosterically by Na+ binding. We also draw attention to a functional polarity that exists in the serine protease fold, which sheds light on the structural linkages between the active site and exosites. [source]


Current knowledge of microRNA characterization in agricultural animals

ANIMAL GENETICS, Issue 3 2010
H.-C. Liu
Summary MicroRNA (miRNA) is a class of single-stranded small (19,24nt) regulatory RNA that silences gene expression post-transcriptionally. miRNAs regulate a wide range of biological processes through the recognition of complementary sequences between miRNAs and their target genes. Profiling studies in livestock have revealed that many miRNAs are species- and tissue-specific, indicating that miRNAs play important roles in essential biological processes in livestock, such as muscle and organ development, the immune response and metabolism. The allelic variation of miRNA target sites and possibly in miRNAs themselves are also likely to be contributing factors to many phenotypic differences in livestock. In this review, we summarize the current miRNA studies undertaken in livestock. [source]