Cloning and sequence analysis of bile salt hydrolase (bsh) gene from Bifidobacterium longum

A pair of PCR primers for the rapid detection of bile salt hydrolase (bsh) gene from Bifidobacterium longum BB536 has been synthesised and have revealed the bsh gene of approx 970 bp in Bifidobacterium longum BB 536 but not in other species of bacteria tested. The bsh gene was cloned and sequenced showing a high similarity to bsh gene previously published. The resulting nucleotide sequence encodes a predicted protein of 317 amino acids, Mw = 35 kDa.     

Proteomic analysis of global changes in protein expression during exposure of gamma radiation in Bacillus sp. HKG 112 isolated from saline soil

A Gram-positive bacterium was isolated from the saline soils of Jangpura (U.P.), India, and showed high-level of radiation-resistant property and survived upto 12.5 kGy dose of gamma radiation. The 16S rDNA sequence of this strain was examined, identified as Bacillus sp. strain HKG 112, and was submitted to the NCBI GenBank (Accession No. GQ925432). The mechanism of radiation resistance and gene level expression were examined by proteomic analysis of whole-cell extract. Two proteins, 38 kDa and 86.5 kDa excised from SDS-PAGE, which showed more significant changes after radiation exposure, were identified by MALDI-TOF as being flagellin and S-layer protein, respectively. Twenty selected 2-DE protein spots from the crude extracts of Bacillus sp. HKG 112, excised from 2- DE, were identified by liquid chromatography mass spectrometry (LC-MS) out of which 16 spots showed significant changes after radiation exposure and might be responsible for the radiation resistance property. Our results suggest that the different responses of some genes under radiation for the expression of radiation-dependent proteins could contribute to a physiological advantage and would be a significant initial step towards a full-system understanding of the radiation stress protection mechanisms of bacteria in different environments.     

Proteomic analysis of changes in mitochondrial protein expression during fruit senescence

Fruit senescence has been reported to be an oxidative phenomenon, but the detailed mechanisms by which ROS regulate this process remain largely unknown. Here we show that senescence process of apple fruit was concomitant with the dynamic alterations in the mitochondrial proteome. Mitochondrial proteins involved in tricarboxylic acid cycle, electron transport chain, carbon metabolism, and stress response were found to be differentially expressed during fruit senescence. Alleviating oxidative stress by lowering the ambient oxygen concentration noticeably decreased the number of changed proteins and delayed fruit senescence, indicating the involvement of ROS in this process. To further investigate the regulatory effect of ROS on senescence process, we analyzed the mitochondrial proteome variations upon exposure to high oxygen (100%), which induces oxidative stress and accelerates fruit senescence. High oxygen treatment led to a further identification of differentially expressed proteins such as mitochondrial manganese superoxide dismutase, an antioxidant scavenging superoxide radicals produced in the mitochondria. Activity of manganese superoxide dismutase was reduced after high oxygen exposure, accompanied by an increase in oxidative protein carbonylation (damaged proteins). These data suggest that ROS may regulate fruit senescence by changing expression profiles of specific mitochondrial proteins and impairing the biological function of these proteins.     

Survival of Bifidobacterium longum immobilized in calcium alginate beads in simulated gastric juices and bile salt solution

Bifidobacterium longum KCTC 3128 and HLC 3742 were independently immobilized (entrapped) in calcium alginate beads containing 2, 3, and 4% sodium alginate. When the bifidobacteria entrapped in calcium alginate beads were exposed to simulated gastric juices and a bile salt solution, the death rate of the cells in the beads decreased proportionally with an increase in both the alginate gel concentration and bead size. The initial cell numbers in the beads affected the numbers of survivors after exposure to these solutions; however, the death rates of the viable cells were not affected. Accordingly, a mathematical model was formulated which expressed the influences of several parameters (gel concentration, bead size, and initial cell numbers) on the survival of entrapped bifidobacteria after sequential exposure to simulated gastric juices followed by a bile salt solution. The model proposed in this paper may be useful for estimating the survival of bifidobacteria in beads and establishing optimal entrapment conditions.     

Characterization of HU-like protein from Bifidobacterium longum

A HU-like protein (HBl) of Bifidobacterium longum was purified and characterized. HBl is heat-stable and acid-resistant, and has a molecular weight of about 9.1 kDa as estimated by its mobility on electrophoresis. HBl is intermediate in basicity (pI 9.8) between the HU-1 and HU-2 proteins of Escherichia coli, and is dissociated from a calf thymus DNA-cellulose column at 300-400 mM NaCl. Its amino acid composition shows many similarities with that of E coli HU. The NH2-terminal amino acid sequence of HBl also shows significant similarities to the consensus sequence deduced from the sequences of eleven HU-like proteins from prokaryotic sources. Chemical crosslinking analysis indicated that the HBl protein predominantly forms a homotypic dimer.     

Structural and functional analysis of a conjugated bile salt hydrolase from Bifidobacterium longum reveals an evolutionary relationship with penicillin V acylase

Bile salt hydrolase (BSH) is an enzyme produced by the intestinal microflora that catalyzes the deconjugation of glycine- or taurine-linked bile salts. The crystal structure of BSH reported here from Bifidobacterium longum reveals that it is a member of N-terminal nucleophil hydrolase structural superfamily possessing the characteristic alphabetabetaalpha tetra-lamellar tertiary structure arrangement. Site-directed mutagenesis of the catalytic nucleophil residue, however, shows that it has no role in zymogen processing into its corresponding active form. Substrate specificity was studied using Michaelis-Menten and inhibition kinetics and fluorescence spectroscopy. These data were compared with the specificity profile of BSH from Clostridium perfrigens and pencillin V acylase from Bacillus sphaericus, for both of which the three-dimensional structures are available. Comparative analysis shows a gradation in activity toward common substrates, throwing light on a possible common route toward the evolution of pencillin V acylase and BSH.     

Labeling of Bifidobacterium longum Cells with 13C-Substituted Leucine for Quantitative Proteomic Analyses

Stable isotope labeling of amino acids in cell culture was used for Bifidobacterium longum. A comprehensive proteomic strategy was developed and validated by designing an appropriate semidefined medium that allows stable replacement of natural leucine by [¹³C₆]leucine. Using this strategy, proteins having variations of at least 50% in their expression rates can be quantified with great confidence.     

Improved tolerance to bile salts of aggregated Bifidobacterium longum produced during continuous culture with immobilized cells

The effect of cell immobilization and continuous culture was studied on selected physiological and technological characteristics of Bifidobacterium longum NCC2705 cultivated for 20 days in a two stage continuous fermentation system. Continuous immobilized cell (IC) cultures with and without glucose limitation exhibited formation of macroscopic cell aggregates after 12 and 9 days, respectively. Auto-aggregation resulted in underestimation of viable cell counts by plate counts by more than 2 log units CFU/ml compared with qPCR method. Modifications of cell membrane composition might partially explain aggregate formation in IC cultures. Decreases in the ratio of unsaturated to saturated fatty acid content from 1.74 to 0.58 might also contribute to the enhanced tolerance of IC cells to porcine bile salts and aminoglycosidic antibiotics compared with free cells from batch cultures.The enhanced resistance against bile salts in combination with auto-aggregation may confer an advantage to probiotic bacteria produced by IC technology.     

长双歧杆菌分泌型表达载体的构建及Tum-5基因的表达

摘要：目的 构建能在双歧杆菌内稳定存在并高效分泌表达外源基因的长双歧杆菌质粒表达载体。方法 以质粒pBAD/glll为基础,以双歧杆菌内源性阿拉伯糖苷酶的分泌性信号肽取代质粒原有的分泌性信号肽,并将双歧杆菌天然质粒的聚合酶基因克隆入载体中,构建表达载体pBBADs。将人Tum-5基因克隆入载体中,构建质粒pBBADs-Tum-5,电转化长双歧杆菌NCC2705,L-阿拉伯糖诱导表达后,Western Blot鉴定基因表达。结果 成功的构建了长双歧杆菌分泌型质粒表达载体,Tum-5基因在双歧杆菌内可以表达。结论 构建的表达载体为双歧杆菌用于肿瘤靶向基因治疗奠定了基础。     

Proteomic analysis of global alteration of protein expression in squamous cell carcinoma of the esophagus

Squamous cell carcinoma of the esophagus (ESCC), a major subtype of esophageal carcinoma, is one of the aggressive cancers with worst prognosis in the world. The dismal outcome of ESCC is attributed to multiple reasons including its aggressive nature, largely unknown molecular mechanism of its progression, and the lack of biomarkers for early detection and effective prediction of its clinical behavior. To identify proteins with prognostic and/or predictive value, we applied a proteomics strategy to quantify proteins differentially expressed in ESCC using matched samples of carcinoma and adjacent normal epithelial cells. The analysis led to identification of 28 proteins aberrantly expressed in cancer cells with changes of at least three-fold in ESCC relative to normal squamous epithelial cells. These changes represent functional alterations of essential proteins for normal cellular physiology, accounting for many cellular changes involved in development of ESCC, including cell transformation, loss of differentiation, tumor growth, apoptosis, tumor invasion, and cell metabolism. The differentially expressed proteins shed new insights on the mechanism of tumorigenesis and provide candidate biomarkers for early detection of ESCC.     

Proteomic analysis of changes in protein expression in liver mitochondria in apoE knockout mice

The involvement of both apolipoprotein E (apoE) and mitochondria in lipid metabolism is widely recognized, however there is surprisingly scarce data about the putative mitochondrial action(s) of this protein. The aim of the study was to screen the alterations in liver mitochondrial proteome caused by apoE deficiency. We applied 2DE-LC-MS/MS methodology to investigate the changes in liver mitochondrial protein expression in 6-months old apoE(-/-) mice as compared to C57BL/6J controls. ApoE(-/-), but not C57BL/6J mice developed visible atherosclerotic changes in aorta and mild, diffuse steatosis of the liver. Collectively, 18 differentially expressed proteins were identified in mitochondria, related to apoptosis, antioxidant and detoxifying mechanisms of mitochondria, as well as lipid metabolism and transport. In conclusion, differential proteomic approach revealed several lines of proteomic evidence that mitochondrial function in the liver of apoE(-/-) mice could be altered as a result of overlapping of pathological and compensatory changes in expression of proteins.     

Efficiency of PCR-based methods in discriminating Bifidobacterium longum ssp. longum and Bifidobacterium longum ssp. infantis strains of human origin

Bifidobacterium longum is considered to play an important role in health maintenance of the human gastrointestinal tract. Probiotic properties of bifidobacterial isolates are strictly strain-dependent and reliable methods for the identification and discrimination of this species at both subspecies and strain levels are thus required. Differentiation between B. longum ssp. longum and B. longum ssp. infantis is difficult due to high genomic similarities. In this study, four molecular-biological methods (species- and subspecies-specific PCRs, random amplified polymorphic DNA (RAPD) method using 5 primers, repetitive sequence-based (rep)-PCR with BOXA1R and (GTG)₅ primers and amplified ribosomal DNA restriction analysis (ARDRA)) and biochemical analysis, were compared for the classification of 30 B. longum strains (28 isolates and 2 collection strains) on subspecies level. Strains originally isolated from the faeces of breast-fed healthy infants (25) and healthy adults (3) showed a high degree of genetic homogeneity by PCR with subspecies-specific primers and rep-PCR. When analysed by RAPD, the strains formed many separate clusters without any potential for subspecies discrimination. These methods together with arabionose/melezitose fermentation analysis clearly differentiated only the collection strains into B. longum ssp. longum and B. longum ssp. infantis at the subspecies level. On the other hand, ARDRA analysis differentiated the strains into the B. longum/infantis subspecies using the cleavage analysis of genus-specific amplicon with just one enzyme, Sau3AI. According to our results the majority of the strains belong to the B. longum ssp. infantis (75%). Therefore we suggest ARDRA using Sau3AI restriction enzyme as the first method of choice for distinguishing between B. longum ssp. longum and B. longum ssp. infantis.     

Proteomic analysis of differential protein expression in atherosclerosis

Although recent studies have shown that several pro-inflammatory proteins can be used as biomarkers for atherosclerosis, the mechanism of atherogenesis is unclear and little information is available regarding proteins involved in development of the disease. Atherosclerotic tissue samples were collected from patients in order to identify the proteins involved in atherogenesis. The protein expression profile of atherosclerosis patients was analysed using two-dimensional electrophoresis-based proteomics. Thirty-nine proteins were detected that were differentially expressed in the atherosclerotic aorta compared with the normal aorta. Twenty-seven of these proteins were identified in the MS-FIT database. They are involved in a number of biological processes, including calcium-mediated processes, migration of vascular smooth muscle cells, matrix metalloproteinase activation and regulation of pro-inflammatory cytokines. Confirmation of differential protein expression was performed by Western blot analysis. Potential applications of the results include the identification and characterization of signalling pathways involved in atherogenesis, and further exploration of the role of selected identified proteins in atherosclerosis.     

Proteomic analysis of differential protein expression in atherosclerosis

Although recent studies have shown that several pro-inflammatory proteins can be used as biomarkers for atherosclerosis, the mechanism of atherogenesis is unclear and little information is available regarding proteins involved in development of the disease. Atherosclerotic tissue samples were collected from patients in order to identify the proteins involved in atherogenesis. The protein expression profile of atherosclerosis patients was analysed using two-dimensional electrophoresis-based proteomics. Thirty-nine proteins were detected that were differentially expressed in the atherosclerotic aorta compared with the normal aorta. Twenty-seven of these proteins were identified in the MS-FIT database. They are involved in a number of biological processes, including calcium-mediated processes, migration of vascular smooth muscle cells, matrix metalloproteinase activation and regulation of pro-inflammatory cytokines. Confirmation of differential protein expression was performed by Western blot analysis. Potential applications of the results include the identification and characterization of signalling pathways involved in atherogenesis, and further exploration of the role of selected identified proteins in atherosclerosis.     

Proteomic analysis of time-dependant difference of protein expression profile changes during neuronal differentiation of mouse embryonic stem cells

The study of ES cell-mediated neuronal differentiation allows elucidating the mechanism of neuronal development in spite of the complexity and the difficult accessibility. During the differentiation of embryonic stem cells into neuronal cell, the expression profiles in the level of protein were extensively investigated by proteomic analysis. These cells were analyzed for charges in proteome during the differentiation of ES cells by 2-dimensional electrophoresis (2-DE) and MALDI-TOF MS. Seven unique proteins were identified, some of which were differentially expressed at each stage. A complex system of neuronal differentiation can be activated in cultured embryonic stem cells and our two dimensional electrophoresis data should be useful for investigating some of the mechanism that regulates neuronal differentiation.     

Proteomic analysis of global protein expression changes in the endothelin-1 rat model for cerebral ischemia: Rescue effect of mild hypothermia

Mild hypothermia is a promising neuroprotective therapy in stroke management. However, little is known about its effects on the global protein expression patterns in brain regions affected by ischemic stroke. We investigated protein expression changes associated with the neuroprotective effects of hypothermia via a functional proteomics approach through the analysis of the core (striatum) and the penumbra (cortex) after an ischemic insult in rats induced by endothelin-1 (Et-1). Functional outcome, infarct volume and related global protein expression changes were assessed 24 h after the insult using two-dimensional difference gel electrophoresis. Mild hypothermia, induced 20 min after endothelin-1 infusion, improved the neurological outcome, reflected by a 36% reduction in infarct volume and a significantly better neurological deficit score. Hypothermia was typically associated with opposite protein expression changes inthe cortex to those induced by stroke under normothermic conditions, but not in the striatum. The main cellular processes rescued by hypothermia and potentially involved in the protection of the cortex are cellular assembly and organization, followed by cell signaling, thereby confirming that hypothermia is neuroprotective through multiple molecular and cellular pathways.     

Differential expression of virulence and stress fitness genes during interaction between Listeria monocytogenes and Bifidobacterium longum

Bifidobacterium is well known to have an inhibitory effect on the survival, growth, and proliferation of various foodborne pathogens, but the mechanism of the molecular action of B. longum in blocking the invasion of Listeria monocytogenes is not yet well defined. In the present study, following RNA extraction and cDNA synthesis, differential expression of virulence and stress fitness genes in L. monocytogenes and B. longum was determined by real-time PCR. The results indicate that L. monocytogenes virulence factors, including actA, hly, inlA, and plcA, showed significantly downregulated expression during co-incubation of B. longum and L. monocytogenes in phosphate-buffered saline. The relative mRNA levels of oppA and serpin, two stress fitness genes in B. longum, were significantly higher than for the control group. These results indicate that downregulation of L. monocytogenes virulence factors during co-incubation with B. longum might be responsible for the inhibitory effects.