Are biters sick? Health status of tail biters in comparison to control pigs

BACKGROUND

Tail biting is a multifactorial problem. As the health status is one of the factors commonly linked to tail biting, this study focuses on the health of identified biters. 30 (obsessive) biters are compared to 30 control animals by clinical and pathological examination as well as blood and cerebrospinal fluid samples. In that way, altogether 174 variables are compared between the groups. Moreover, connections between the variables are analysed.

RESULTS

In the clinical examination, 6 biters, but only 2 controls (P = 0.019) were noticeably agitated in the evaluation of general behaviour, while 8 controls were noticeably calmer (2 biters, P = 0.02). Biters had a lower body weight (P = 0.0007) and 13 biters had overlong bristles (4 controls, P = 0.008). In the pathological examination, 5 biters, but none of the controls had a hyperceratosis or inflammation of the pars proventricularis of the stomach (P = 0.018). However, 7 controls and only 3 biters were affected by gut inflammation (P = 0.03). In the blood sample, protein and albumin levels were below normal range for biters (protein: 51.6 g/l, albumin: 25.4 g/l), but not for controls (protein: 53.7 g/l, albumin: 27.4 g/l), (protein: P = 0.05, albumin: P = 0.02). Moreover, 14 biters, but only 8 controls had poikilocytosis (P = 0.05). Although not statistically different between groups, many animals (36/60) were affected by hypoproteinemia and hyponatremia as well as by hypokalemia (53/60) and almost all animals (58/60) had hypomagnesemia. For hypomagnesemia, significant connections with variables linked to tail damage and ear necrosis were detected (r_s/V/ρ ≥ 0.4, P ≤ 0.05).

CONCLUSION

The results suggest that behavioural tests might be helpful in identifying biters. Moreover, cornification and inflammation of the pars proventricularis is linked to becoming a biter. Furthermore, the results highlight the need for appropriate and adjusted nutrient and mineral supply, especially with regard to magnesium.

Retrospective evaluation of surgical technique, complications and long-term outcome of lateral and medial humeral condylar fractures in 80 dogs

CASE HISTORY

Medical records of a single veterinary teaching hospital in Giessen, Germany were retrospectively reviewed for dogs presented for medial or lateral humeral condylar fractures (HCF) between 2007 and 2019. Data regarding surgical technique and complications were collected from the medical records. The latter was supplemented through information obtained from telephone interviews with referral veterinarians and from an owner questionnaire completed ≥12 months after surgical repair, which also provided data regarding outcome.

CLINICAL FINDINGS

Eighty dogs with 85 HCF were identified: 13 (15.3%) HCF were medial (bilateral in two dogs) and 72 (84.7%) were lateral (bilateral in three dogs). French Bulldogs (n = 19/80; 23.8%) were most commonly affected. Patients were predominantly skeletally immature and light-weight, with a median age at the time of presentation of 3 (min 2, max 118) months and with a median body weight of 6.4 (min 1, max 46) kg. There were 38 female (47.5%) and 42 male (52.5%) dogs. Fractures developed most frequently secondary to minor trauma (67/77; 87.0%). Dogs were presented in 35/84 (41.7%) cases more than 24 hours after fracture occurrence.

TREATMENT AND OUTCOME

Surgical treatment was performed in 80/85 (94.1%) HCF. An open reduction and internal fixation approach was chosen in all cases. A transcondylar screw (TS) combined with a supracondylar (SC) K-wire (67/80; 83.8%) was the most frequently used fixation technique. Considering all fracture fixation methods, complications (26/80; 32.5%) were classed as minor in 10 (12.5%), major in 14 (17.5%) and catastrophic in two (2.5%) of the 80 surgically treated HCF. Long-term outcome was excellent in 68.6% (24/35 HCF) and very good in 22.9% (8/35 HCF) of the cases for which follow-up information was obtained. Additionally, owner information revealed that 85.7% of dogs (30/35 HCF) were free of lameness in the long-term.

CLINICAL RELEVANCE

This case series demonstrates that surgical repair of lateral and medial HCF with a TS and SC K-wire is a viable option to consider in skeletally immature and light-weight patients. Complications occur frequently after surgical fixation of HCF, but owners can expect a very good to excellent long-term outcome in the majority of cases.

Evaluation of consistency over time of the use of the Animal Welfare Indicators protocol for horses

Consistency over time is a basic requirement for welfare assessment schemes since consistency must not depend, for example, on the day it is carried out. This study analysed the consistency of the indicators of the Animal Welfare Indicators (AWIN) protocol for horses (Equus caballus) over time. Given the multi-dimensionality of animal welfare, the AWIN protocol includes a variety of indicators evaluating, eg the health status or the behaviour of the animals. Fourteen establishments keeping horses in Germany were visited four times each (day 0, day 3, day 42, day 90). For the evaluation of reliability and agreement between the different visits, ie across time, the reference visit on day 0 was compared to the other visits via calculation of Spearman's rank correlation (RS), intra-class correlation (ICC), smallest detectable change (SDC) and limits of agreement (LoA). The indicator, Qualitative Behaviour Assessment (QBA) was analysed by Principal Component Analysis (PCA). Most of the indicators demonstrated sufficient consistency over time. Indicators that were inconsistent included parts of the Horse Grimace Scale, outcomes of behavioural tests, the presence of swollen joints as well as the indicators hoof neglect, alopecia on the legs and water cleanliness. The QBA was consistent for the period of 42 days, but not for 90 days. Overall, those indicators with insufficient consistency over time require to be revised or replaced in future welfare assessment schemes.

Dynamic proteomic analysis of Phanerochaete chrysosporium under copper stress

The model white rot fungus Phanerochaete chrysosporium is frequently preferred for heavy metal accumulation studies due to its high resistance to heavy metals, including copper (Cu). Here, the response of P. chrysosporium under Cu stress at different time points was investigated for the first time by a detailed proteomic analysis using 2DE MALDI-TOF/MS and nanoLC-MS/MS techniques. A total of 123 Cu-responsive protein spots were determined using 2DE approach, and 104 of them were corresponded to 73 distinct open reading frames (ORFs). Of identified ones, 88 spots were over-, and 16 spots were underrepresented. The majority of these proteins showed to the strongest response at 8th h of Cu exposure. Using nanoLC-MS/MS analysis, a total of 167 differentially produced proteins were identified from Cu-exposed cultures after enrichment of the membrane proteins followed by SILAC. Seventy four, 66, and 69 overrepresented, and 56, 71, and 64 underrepresented proteins were identified at 2 h, 4 h, and 8 h of Cu exposure, respectively. The bioinformatic analysis of these proteins revealed that intracellular trafficking proteins such as Ran GTPase and a p24 family protein, and certain proteins involved in posttranslational modification, protein turnover and folding were Cu-responsive. Three important transcription factors (TFs), NAC, BTF3, and homeobox TFs, 40S and 60S ribosomal proteins, chaperones such as Hsp26/Hsp42 and mortalin, as well as 20S proteasome, 14-3-3 proteins and Hsp90 involve in Cu-stress response of P. chrysosporium. Moreover, certain elements of translation machinery, the proteins related with aspartate, methionine, and pyruvate metabolisms, transketolase, and trehalase related with carbohydrate metabolism, citrate synthase, fumarase, V-ATPase, and F0F1-type ATPase playing role in energy production and conversion, transport proteins such as multidrug resistance and p24 family proteins as well as actin-related proteins involved in cytoskeleton remodeling were determined to be Cu-responsive. The present proteome analysis revealed that P. chrysosporium mainly regulates translational and posttranslational processes, certain transport processes, many metabolic pathways and cytoskeleton to overcome the Cu-induced oxidative stress.

An Easy and Fast Protocol for Affinity Bead-Based Protein Enrichment and Storage of Proteome Samples

Analysis of dilute protein samples is a challenging task for scientific and industrial labs all over the world. Although there are different methods available that allow for protein enrichment from various biological sources, all of them have serious limitations apart from their advantages. In order to perform highly reproducible and sensitive protein analysis of lowest concentrated samples, we optimized a method to enrich proteins on affinity beads (StrataClean) recently. This chapter describes the general protocol of this strategy, thereby discussing the power as well as the limits of this technique for qualitative and quantitative proteomic studies. Moreover, additional application and protocol variants will be discussed, expanding the number of compatible up- and downstream processing techniques compared to the originally published method. Hence, we evaluated the reduction of time for sample preparation by use of preprimed affinity beads and shorter incubation durations as well as the influence of high concentration of salts or urea in the sample buffer.

Interobserver reliability of the 'Welfare Quality(®) Animal Welfare Assessment Protocol for Growing Pigs'

The present paper focuses on evaluating the interobserver reliability of the 'Welfare Quality(®) Animal Welfare Assessment Protocol for Growing Pigs'. The protocol for growing pigs mainly consists of a Qualitative Behaviour Assessment (QBA), direct behaviour observations (BO) carried out by instantaneous scan sampling and checks for different individual parameters (IP), e.g. presence of tail biting, wounds and bursitis. Three trained observers collected the data by performing 29 combined assessments, which were done at the same time and on the same animals; but they were carried out completely independent of each other. The findings were compared by the calculation of Spearman Rank Correlation Coefficients (RS), Intraclass Correlation Coefficients (ICC), Smallest Detectable Changes (SDC) and Limits of Agreements (LoA). There was no agreement found concerning the adjectives belonging to the QBA (e.g. active: RS: 0.50, ICC: 0.30, SDC: 0.38, LoA: -0.05 to 0.45; fearful: RS: 0.06, ICC: 0.0, SDC: 0.26, LoA: -0.20 to 0.30). In contrast, the BO showed good agreement (e.g. social behaviour: RS: 0.45, ICC: 0.50, SDC: 0.09, LoA: -0.09 to 0.03 use of enrichment material: RS: 0.75, ICC: 0.68, SDC: 0.06, LoA: -0.03 to 0.03). Overall, observers agreed well in the IP, e.g. tail biting (RS: 0.52, ICC: 0.88; SDC: 0.05, LoA: -0.01 to 0.02) and wounds (RS: 0.43, ICC: 0.59, SDC: 0.10, LoA: -0.09 to 0.10). The parameter bursitis showed great differences (RS: 0.10, ICC: 0.0, SDC: 0.35, LoA: -0.37 to 0.40), which can be explained by difficulties in the assessment when the animals moved around quickly or their legs were soiled. In conclusion, the interobserver reliability was good in the BO and most IP, but not for the parameter bursitis and the QBA.

Review of the assessment of animal welfare with special emphasis on the "Welfare Quality^® animal welfare assessment protocol for growing pigs"

Abstract. This paper discusses the arising need for an objective, but feasible, reliable and valid method for assessing animal welfare on farms. Animal welfare has become especially important since the industrialisation of animal housing after the Second World War and as public awareness and concern has increased. Simultaneously, alienation of the public from agriculture has taken place, as the population has moved increasingly from rural areas to towns. This has led to a very emotional discussion concerning the welfare of farmed animals, and thus a need for not only a clear definition but also a way of objectively measuring it has arisen. It is probably best defined as a total of the different conceptions health, natural behaviour and positive affective state. In the last few years, different methods for an objective assessment have been developed; however, all of them still face great challenges in their practical implementation and acceptance. The most promising method is probably the Welfare Quality® (WQ) approach, especially as it concentrates on animal-based parameters. The development of the WQ protocols emphasised not only the different conceptions of animal welfare but also especially the feasibility, reliability and validity of the parameters to be included. One of the main challenges of these protocols remains, however, the final aggregation of the results to a welfare score. Furthermore, a thorough cost–benefit analysis has not been carried out so far. Even more importantly, only a few studies have addressed the general reliability and validity of the complete protocols, and those studies that have addressed these issues have also revealed challenges concerning the interobserver and test–retest reliability of some of the included parameters. As an example, this is discussed in detail for the "Welfare Quality® animal welfare assessment protocol for growing pigs". In conclusion, the WQ approach can be seen as promising, but it has also revealed that there are still a considerable number of challenges that need to be addressed in further studies on the WQ protocols in order to achieve constant improvement. These challenges should be borne in mind in the application of these protocols, which should not be simply referred to as a gold standard.

Picking vanished proteins from the void: how to collect and ship/share extremely dilute proteins in a reproducible and highly efficient manner

Successful proteome analyses of highly dilute samples are strongly dependent on optimized workflows considering especially sample preparation prior to highly sensitive mass spectrometric analysis. Various methods are available for enrichment of proteome samples, each characterized by specific advantages and disadvantages limiting their general application as a method of choice. Here we suggest an optimized universal protocol ensuring reproducibility and effective enrichment of dilute samples by commercial affinity beads. By comparably assessing the performance of the new protocol with selected standard enrichment techniques, we show the seamless application of the enrichment in common mass spectrometry based proteomic workflows. Further, novel applications are suggested including a facile storage and shipping of desiccated, trapped proteome samples at ambient temperatures and usage of the affinity beads for gel-free proteomic approaches.

Comprehensive absolute quantification of the cytosolic proteome of Bacillus subtilis by data independent, parallel fragmentation in liquid chromatography/mass spectrometry (LC/MS(E))

In the growing field of systems biology, the knowledge of protein concentrations is highly required to truly understand metabolic and adaptational networks within the cells. Therefore we established a workflow relying on long chromatographic separation and mass spectrometric analysis by data independent, parallel fragmentation of all precursor ions at the same time (LC/MS(E)). By prevention of discrimination of co-eluting low and high abundant peptides a high average sequence coverage of 40% could be achieved, resulting in identification of almost half of the predicted cytosolic proteome of the Gram-positive model organism Bacillus subtilis (>1,050 proteins). Absolute quantification was achieved by correlation of average MS signal intensities of the three most intense peptides of a protein to the signal intensity of a spiked standard protein digest. Comparative analysis with heavily labeled peptides (AQUA approach) showed the use of only one standard digest is sufficient for global quantification. The quantification results covered almost four orders of magnitude, ranging roughly from 10 to 150,000 copies per cell. To prove this method for its biological relevance selected physiological aspects of B. subtilis cells grown under conditions requiring either amino acid synthesis or alternatively amino acid degradation were analyzed. This allowed both in particular the validation of the adjustment of protein levels by known regulatory events and in general a perspective of new insights into bacterial physiology. Within new findings the analysis of "protein costs" of cellular processes is extremely important. Such a comprehensive and detailed characterization of cellular protein concentrations based on data independent, parallel fragmentation in liquid chromatography/mass spectrometry (LC/MS(E)) data has been performed for the first time and should pave the way for future comprehensive quantitative characterization of microorganisms as physiological entities.

Simplification and improvement of protein detection in two-dimensional electrophoresis gels with SERVA HPE™ lightning red

A new fluorescent amino-reactive dye has been tested for both labelling proteins prior to electrophoretic separations and between the two steps of two-dimensional electrophoresis. A series of experiments showed, that the labelling of lysines with this dye is compatible with all standard additives used for sample preparation, including reducing substances and carrier ampholytes. Using this dye for pre-labelling considerably simplifies the electrophoresis and detection workflow and provides highly sensitive and quantitative visualisation of proteins.

Global relative quantification with liquid chromatography-matrix-assisted laser desorption ionization time-of-flight (LC-MALDI-TOF)--cross-validation with LTQ-Orbitrap proves reliability and reveals complementary ionization preferences

Quantitative LC-MALDI is an underrepresented method, especially in large-scale experiments. The additional fractionation step that is needed for most MALDI-TOF-TOF instruments, the comparatively long analysis time, and the very limited number of established software tools for the data analysis render LC-MALDI a niche application for large quantitative analyses beside the widespread LC-electrospray ionization workflows. Here, we used LC-MALDI in a relative quantification analysis of Staphylococcus aureus for the first time on a proteome-wide scale. Samples were analyzed in parallel with an LTQ-Orbitrap, which allowed cross-validation with a well-established workflow. With nearly 850 proteins identified in the cytosolic fraction and quantitative data for more than 550 proteins obtained with the MASCOT Distiller software, we were able to prove that LC-MALDI is able to process highly complex samples. The good correlation of quantities determined via this method and the LTQ-Orbitrap workflow confirmed the high reliability of our LC-MALDI approach for global quantification analysis. Because the existing literature reports differences for MALDI and electrospray ionization preferences and the respective experimental work was limited by technical or methodological constraints, we systematically compared biochemical attributes of peptides identified with either instrument. This genome-wide, comprehensive study revealed biases toward certain peptide properties for both MALDI-TOF-TOF- and LTQ-Orbitrap-based approaches. These biases are based on almost 13,000 peptides and result in a general complementarity of the two approaches that should be exploited in future experiments.

Characterization of proteome alterations in Phanerochaete chrysosporium in response to lead exposure

BACKGROUND

Total soluble proteome alterations of white rot fungus Phanerochaete chrysosporium in response to different doses (25, 50 and 100 μM) of Pb (II) were characterized by 2DE in combination with MALDI-TOF-MS.

RESULTS

Dose-dependent molecular response to Pb (II) involved a total of 14 up-regulated and 21 down-regulated proteins. The induction of an isoform of glyceraldehyde 3-phosphate dehydrogenase, alcohol dehydrogenase class V, mRNA splicing factor, ATP-dependent RNA helicase, thioredoxin reductase and actin required a Pb (II) dose of at least 50 μM. Analysis of the proteome dynamics of mid-exponential phase cells of P. chrysosporium subjected to 50 μM lead at exposure time intervals of 1, 2, 4 and 8 h, identified a total of 23 proteins in increased and 67 proteins in decreased amount. Overall, the newly induced/strongly up-regulated proteins involved in (i) amelioration of lipid peroxidation products, (ii) defense against oxidative damage and redox metabolism, (iii) transcription, recombination and DNA repair (iv) a yet unknown function represented by a putative protein.

CONCLUSION

The present study implicated the particular role of the elements of DNA repair, post-tanscriptional regulation and heterotrimeric G protein signaling in response to Pb (II) stress as shown for the first time for a basidiomycete.

Quality control of inclusion bodies in Escherichia coli

Background

Bacterial inclusion bodies (IBs) are key intermediates for protein production. Their quality affects the refolding yield and further purification. Recent functional and structural studies have revealed that IBs are not dead-end aggregates but undergo dynamic changes, including aggregation, refunctionalization of the protein and proteolysis. Both, aggregation of the folding intermediates and turnover of IBs are influenced by the cellular situation and a number of well-studied chaperones and proteases are included. IBs mostly contain only minor impurities and are relatively homogenous.

Results

IBs of α-glucosidase of Saccharomyces cerevisiae after overproduction in Escherichia coli contain a large amount of (at least 12 different) major product fragments, as revealed by two-dimensional polyacrylamide gel electrophoresis (2D PAGE). Matrix-Assisted-Laser-Desorption/Ionization-Time-Of-Flight Mass-Spectrometry (MALDI-ToF MS) identification showed that these fragments contain either the N- or the C-terminus of the protein, therefore indicate that these IBs are at least partially created by proteolytic action. Expression of α-glucosidase in single knockout mutants for the major proteases ClpP, Lon, OmpT and FtsH which are known to be involved in the heat shock like response to production of recombinant proteins or to the degradation of IB proteins, clpP, lon, ompT, and ftsH did not influence the fragment pattern or the composition of the IBs. The quality of the IBs was also not influenced by the sampling time, cultivation medium (complex and mineral salt medium), production strategy (shake flask, fed-batch fermentation process), production strength (T5-lac or T7 promoter), strain background (K-12 or BL21), or addition of different protease inhibitors during IB preparation.

Conclusions

α-glucosidase is fragmented before aggregation, but neither by proteolytic action on the IBs by the common major proteases, nor during downstream IB preparation. Different fragments co-aggregate in the process of IB formation together with the full-length product. Other intracellular proteases than ClpP or Lon must be responsible for fragmentation. Reaggregation of protease-stable α-glucosidase fragments during in situ disintegration of the existing IBs does not seem to occur.

Towards the entire proteome of the model bacterium Bacillus subtilis by gel-based and gel-free approaches

With the emergence of mass spectrometry in protein science and the availability of complete genome sequences, proteomics has gone through a rapid development. The soil bacterium Bacillus subtilis, as one of the first DNA sequenced species, represents a model for Gram-positive bacteria and its proteome was extensively studied throughout the years. Having the final goal to elucidate how life really functions, one basic requirement is to know the entirety of cellular proteins. This review presents how far we have got in unraveling the proteome of B. subtilis. The application of gel-based and gel-free technologies, the analyses of different subcellular proteome fractions, and the pursuance of various physiological strategies resulted in a coverage of more than one-third of B. subtilis theoretical proteome.

Gel-free and Gel-based Proteomics in Bacillus subtilis

The proteome of exponentially growing Bacillus subtilis cells was dissected by the implementation of shotgun proteomics and a semigel-based approach for a particular exploration of membrane proteins. The current number of 745 protein identifications that was gained by the use of two-dimensional gel electrophoresis could be increased by 473 additional proteins. Therefore, almost 50% of the 2500 genes expressed in growing B. subtilis cells have been demonstrated at the protein level. In terms of exploring cellular physiology and adaptation to environmental changes or stress, proteins showing an alteration in expression level are of primary interest. The large number of vegetative proteins identified by gel-based and gel-free approaches is a good starting point for comparative physiological investigations. For this reason a gel-free quantitation with the recently introduced iTRAQ (isobaric tagging for relative and absolute quantitation) reagent technique was performed to investigate the heat shock response in B. subtilis. A comparison with gel-based data showed that both techniques revealed a similar level of up-regulation for proteins belonging to well studied heat hock regulons (SigB, HrcA, and CtsR). However, additional datasets have been obtained by the gel-free approach indicating a strong heat sensitivity of specific enzymes involved in amino acid synthesis.

Proteome analyses of Staphylococcus aureus in growing and non-growing cells: a physiological approach

Staphylococcus aureus is a versatile human pathogen causing a wide variety of diseases ranging from wound infection to endocarditis, osteomyelitis, and sepsis. In order to investigate this pathogen, we sought to analyze the cytoplasmic proteome of S. aureus COL by using two different approaches: two-dimensional (2D) gel analyses combined with matrix-assisted laser ionization-time of flight mass spectrometry and a gel-free system using multidimensional liquid chromatography followed by mass spectrometry. By combining both analyses we identified 1123 cytoplasmic proteins that represent two-thirds of the cytoplasmic proteome of the organism. With our standard 2D gel setup (pI 4-7) we identified 473 proteins that cover about 40% of the cytoplasmic proteome predicted for this proteomic window. The identified proteins belong to a variety of cellular functions ranging from the transcriptional and translational machinery, tricarboxylic acid cycle (TCC), glycolysis, and fermentation pathways to biosynthetic pathways of nucleotides, fatty acids, and cell wall components. While most of the metabolic pathways predicted for S. aureus were covered by this gel-based proteomics 650 additional proteins were identified by the gel-free approach, among them alkaline or hydrophobic proteins. In our work, we established a master 2D gel that enabled us to study the regulation of core carbon metabolism in S. aureus cells grown in a complex medium. Our comparison of the protein pattern of exponentially growing cells with that of stationary-phase cells revealed a higher amount of enzymes involved in protein synthesis, transcription, and glycolysis in exponentially growing cells. In contrast, enzymes of the TCC and gluconeogenesis are increased at the stationary phase. With this comprehensive proteome map we have an essential tool for a better understanding of cell physiology of the human pathogen, S. aureus.

A comprehensive proteome map of growing Bacillus subtilis cells

The proteome of growing cells of Bacillus subtilis was analyzed in order to provide the basis for its application in microbial physiology. DNA arrays were used to calculate the number of genes transcribed in growing cells. From the 4100 B. subtilis genes, 2515 were actively transcribed in cells grown under standard conditions. From these genes 1544 proteins should be covered by our standard gel system pI 4-7. Using this standard gel system and supplementary zoom gels (pI 5.5-6.7, 5-6, 4.5-5.5, and 4-5) 693 proteins which are expressed in growing cells were detected that cover more than 40% of the vegetative proteome predicted for this region. Particularly broad coverage and thus comprehensive monitoring will be possible for central carbohydrate metabolism (glycolysis, pentose phosphate shunt, and citric acid cycle), amino acid synthesis pathways, purine and pyrimidine metabolism, fatty acid metabolism, and main cellular functions like replication, transcription, translation, and cell wall synthesis. Comparing the theoretical pI and Mr values with those experimentally determined a reasonable correlation was found for the majority of protein spots. By a color code outliers with dramatic deviations in charge or mass were visualized that may indicate post-translational modifications. In addition to the cytosolic neutral and alkaline proteins, 130 membrane proteins were found relying on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) separation in combination with electrospray ionization-tandem mass spectrometry (ESI-MS/MS) techniques. The vegetative proteome containing 876 proteins in total is now ready for physiological applications. Two main proteome fractions (pI 4-7 and zoom gel pI 4.5-5.5) should be sufficient for such high-throughput physiological proteomics.

Probing the active site of homoserine trans-succinylase

Homoserine trans-succinylase is the first enzyme in methionine biosynthesis of Escherichia coli and catalyzes the activation of homoserine via a succinylation reaction. The in vivo activity of this enzyme is subject to tight regulation by several mechanisms, including repression and activation of gene expression, feedback inhibition, temperature regulation and proteolysis. This complex regulation reflects the key role of this enzyme in bacterial metabolism. Here, we demonstrate--using proteomics and high-resolution mass spectrometry--that succinyl is covalently bound to one of the two adjacent lysine residues at positions 45 and 46. Replacing these lysine residues by alanine abolished the enzymatic activity. These findings position the lysine residues, one of which is conserved, at the active site.

Two-dimensional reference map of Agrobacterium tumefaciens proteins

Proteomics based on two-dimensional (2-D) gel electrophoresis of proteins followed by spot identification with mass spectrometry is a commonly used method for physiological studies. Physiological proteomics requires 2-D reference maps, on which most of the main proteins are identified. We present a reference map for the bacterial plant pathogen Agrobacterium tumefaciens proteins, which contains more than 300 entries with an isoelectric point (pI) between 4 and 7. The quantitative study of the proteins in the analytical window of the master gel demonstrated unique features, in comparison with other bacteria. In addition, a theoretical analysis of several protein parameters was performed and compared with the experimental results. A comparison of the theoretical molecular weight (MW) of the proteins and their theoretical pI with their vertical and horizontal migration distances, respectively, pointed out the existence of several proteins that strongly diverted from the graph trend-line. These proteins were clearly subjected to post-translational modifications, which changed their pI and/or MW. Additional support for post-translational modifications comes from the identification of multiple spots of the same gene products. Post-translational modifications appear to be more common than expected, at least for soluble proteins, as more than 10% of the proteins were associated with multiple spots.

Highly phosphorylated bacterial proteins

We show in Gram-negative and Gram-positive bacteria the appearance of highly acidic proteins, which are highly phosphorylated. This group of proteins includes many cellular proteins, such as chaperones, biosynthetic, and metabolic enzymes. These proteins accumulate under stress conditions or under conditions, which overload the proteolytic system. Pulse chase experiments using radioactive phosphate indicate that the phosphorylated proteins have a short half-life, suggesting that they could be degradation intermediates. Moreover, results from in vitro experiments in Escherichia coli indicated that ribosomal proteins become susceptible to proteolysis after polyphosphorylation. Therefore, it is possible that the highly phosphorylated proteins represent a group of proteins tagged for degradation by phosphorylation. Such a tagging process may be involved in a general bacterial degradation pathway.

Analysis of Automatically Generated Peptide Mass Fingerprints of Cellular Proteins and Antigens from Helicobacter pylori 26695 Separated by Two-dimensional Electrophoresis

Helicobacter pylori is a causative agent of severe diseases of the gastric tract ranging from chronic gastritis to gastric cancer. Cellular proteins of H. pylori were separated by high resolution two-dimensional gel electrophoresis. A dataset of 384 spots was automatically picked, digested, spotted, and analyzed by matrix-assisted laser desorption ionization mass spectrometry peptide mass fingerprint in triple replicates. This procedure resulted in 960 evaluable mass spectra. Using a new version of our data analysis software MS-Screener we improved identification and tested reliability of automatically generated data by comparing with manually produced data. Antigenic proteins from H. pylori are candidates for vaccines and diagnostic tests. Previous immunoproteomics studies of our group revealed antigen candidates, and 24 of them were now closely analyzed using the MS-Screener software. Only in three spots minor components were found that may have influenced their antigenicities. These findings affirm the value of immunoproteomics as a hypothesis-free approach. Additionally, the protein species distribution of the known antigen GroEL was investigated, dimers of the protein alkyl hydroperoxide reductase were found, and the fragmentation of gamma-glutamyltranspeptidase was demonstrated.

The role of peptide deformylase in protein biosynthesis: a proteomic study

Recently we investigated the influence of classical and emerging antibiotics on the proteome of Bacillus subtilis including in our studies actinonin, a potent novel inhibitor of peptide deformylase. The protein synthesis pattern under actinonin treatment changed so dramatically that a direct comparison to the control pattern was impossible. Dual channel imaging revealed that actinonin treatment caused the majority of newly synthesised proteins to accumulate in spots different from the ones usually observed, indicating a more acidic isoelectric point. Two strategies were used to investigate the nature of the charge shift. In the first place, protein patterns of a conditional peptide deformylase mutant under nonrepressing and repressing conditions were compared. Secondly, several protein pairs excised from two-dimensional (2-D) gels of the peptide deformylase mutant, exponentially growing untreated wild-type and the actinonin treated wild-type were investigated with matrix-assisted laser desorption/ionization and electrospray ionization (ESI) time of flight mass spectrometry (TOF MS) for the existence of N-terminal formylation. Under nonrepressing conditions the mutant protein pattern resembled that of the wild-type. The loss of peptide deformylase activity under repressing conditions led to the same pI shift observed for actinonin treatment in the wild-type. Quadrupole TOF-MS on 11 protein pairs proved that the remaining N-terminal formyl residue was indeed responsible for the charge shift. Eight of these protein pairs were also present on 2-D gels of exponentially growing B. subtilis, where the more acidic, still formylated protein species represented the smaller parts.

Transcriptome and proteome analysis of Bacillus subtilis gene expression modulated by amino acid availability

A comprehensive study of Bacillus subtilis gene expression patterns in response to amino acid availability was performed by means of proteomics and transcriptomics. The methods of two-dimensional protein gel electrophoresis and DNA macroarray technology were combined to analyze cells exponentially grown in minimal medium with and without 0.2% Casamino Acids (CAA). This approach revealed about 120 genes predominantly involved in amino acid biosynthesis, sporulation, and competence, which were downregulated in CAA-containing medium. Determination of sporulation frequencies confirmed the physiological relevance of the expression data.

Role of the general stress response during strong overexpression of a heterologous gene in Escherichia coli

The strong overexpression of heterologous genes in Escherichia coli often leads to inhibition of cell growth, ribosome destruction, loss of culturability, and induction of stress responses, such as a heat shock-like response. Here we demonstrate that the general stress response, which is connected to the stress response regulator sigmas (sigma38, rpoS gene product), is suppressed during strong overproduction of a heterologous alpha-glucosidase. The mRNA levels of the rpoS and osmY stress genes drastically decrease after induction of the strong overexpression system. It is shown that an rpoS mutation causes a significant loss of cell viability after induction of the expression system. Furthermore, it is demonstrated that an E. coli c/pP mutant, which could be suggested to improve heterologous protein production, is not a good production host if a tac-promoter is used to control the expression of the recombinant gene. Data from this study suggest that the overexpression of the alpha-glucosidase was greatly decreased by sigma factor competition in the clpP mutant, due to the increased sigmas level in this mutant background.

Heat shock proteome of Agrobacterium tumefaciens: evidence for new control systems

The regulation of Agrobacterium tumefaciens heat shock genes involves a transcriptional activator (RpoH) and repressor elements (HrcA-CIRCE). Using proteome analysis and mutants in these control elements, we show that the heat shock induction of 32 (out of 56) heat shock proteins is independent of RpoH and HrcA. These results indicate the existence of additional regulatory factors in the A. tumefaciens heat shock response.

A comprehensive two-dimensional map of cytosolic proteins of Bacillus subtilis

Proteomics relying on two-dimensional (2-D) gel electrophoresis of proteins followed by spot identification with mass spectrometry is an excellent experimental tool for physiological studies opening a new perspective for understanding overall cell physiology. This is the intriguing outcome of a method introduced by Klose and O'Farrell independently 25 years ago. Physiological proteomics requires a 2-D reference map on which most of the main proteins were identified. In this paper, we present such a reference map with more than 300 entries for Bacillus subtilis proteins with an isoelectric point (pI) between 4 and 7. The most abundant proteins of exponentially growing cells were compiled and shown to perform mainly housekeeping functions in glycolysis, tricarboxylic acid cycle (TCC), amino acid biosynthesis and translation as well as protein quality control. Furthermore, putative post-translational modifications were shown at a large scale, with 47 proteins in total forming more than one spot. In a few selected cases evidence for phosphorylation of these proteins is presented. The proteome analysis in the standard pI range was complemented by either stretching the most crowded regions in a narrow pH gradient 4.5-5.5, or by adding other fractions of the total B. subtilis proteome such as alkaline proteins as well as extracellular proteins. A big challenge for future studies is to provide an experimental protocol covering the fraction of intrinsic membrane proteins that almost totally escaped detection by the experimental procedure used in this study.

Stress-induced proteins of Agrobacterium tumefaciens

The pattern of proteins produced by bacteria represents the physiological state of the organism as well as the environmental conditions encountered. Environmental stress induces the expression of several regulons encoding stress proteins. Extensive information about the proteins which constitute these regulons (or stimulons) and their control is available for very few bacteria, such as the Gram-positive Bacillus subtilis and the Gram-negative Escherichia coli (gamma-proteobacteria) and is minimal for all other bacteria. Agrobacterium tumefaciens is a Gram-negative plant pathogen of the alpha-proteobacteria, which constitutes the main tool for plant recombinant genetics. Our previous studies on the control of chaperone-coding operons indicated that A. tumefaciens has unique features and combines regulatory elements from both B. subtilis and E. coli. Therefore, we examined the patterns of proteins induced in A. tumefaciens by environmental changes using two-dimensional gel electrophoresis and dual-channel image analysis. Shifts to high temperature, oxidative and mild acid stresses stimulated the expression of 97 proteins. The results indicate that most of these stress-induced proteins (80/97) were specific to one stress stimulon. Only 10 proteins appear to belong to a general stress regulon.

Vascular extracellular superoxide dismutase activity in patients with coronary artery disease: relation to endothelium-dependent vasodilation

BACKGROUND

Increased inactivation of nitric oxide by oxygen free radicals contributes to endothelial dysfunction in patients with coronary artery disease (CAD). We therefore determined the activity of extracellular superoxide dismutase (EC-SOD), the major antioxidant enzyme system of the vessel wall, and its relation to flow-dependent, endothelium-mediated dilation (FDD) in patients with CAD.

METHODS AND RESULTS

SOD isoenzyme activity was determined in coronary arteries from 10 patients with CAD and 10 control subjects. In addition, endothelium-bound EC-SOD activity (eEC-SOD), released by heparin bolus injection, and FDD of the radial artery were measured in 35 patients with CAD and 15 control subjects. FDD, determined by high-resolution ultrasound, was assessed at baseline, after intra-arterial infusion of vitamin C, N-monomethyl-L-arginine, and combination of both. EC-SOD activity in coronary arteries (control subjects: 126+/-14; CAD: 63+/-11 U/mg protein; P<0.01) and eEC-SOD activity in vivo (control subjects: 14.5+/-1.1; CAD: 3.8+/-1.1 U. mL(-1). min(-1); P<0.01) were reduced in patients with CAD. Activity of eEC-SOD was positively correlated with FDD (r=0.47; P<0. 01) and negatively with the effect of the antioxidant vitamin C on FDD (r=-0.59; P<0.01). In young individuals with hypercholesterolemia, however, eEC-SOD activity was increased (21. 0+/-1.2 U. mL(-1). min(-1); n=10; P<0.05).

CONCLUSIONS

In patients with CAD, vascular EC-SOD activity is substantially reduced. The close relation between endothelium-bound EC-SOD activity and FDD suggests that reduced EC-SOD activity contributes to endothelial dysfunction in patients with CAD. In young hypercholesterolemic individuals, however, endothelium-bound EC-SOD activity is increased and may, in part, counteract impairment of endothelial function as the result of increased formation of oxygen free radicals.

Dual channel imaging of two-dimensional electropherograms in Bacillus subtilis

The allocation of proteins to stimulons and regulons is an essential step towards the understanding of the global regulation of the expression of entire genomes. The computer-aided evaluation and matching of two-dimensional protein gels loaded with radioactively labeled proteins from exponentially growing or stressed cells is a useful but time-consuming procedure for the description of stimulons and regulons. This paper describes the dual-channel image analysis that offers the opportunity to visualize the content and synthesis rate of a whole set of bacterial proteins on a single electropherogram. By pulse-labeling with L-[35S]methionine, the protein synthesis pattern (red color) can be directly compared with the protein level pattern (green color). Because matching of other gels can be avoided, this new technique is useful for the rapid search for proteins that belong to different stimulons or regulons. This approach was tested for the identification of proteins of heat stress or oxidative stress stimulons. Proteins that were induced by heat or oxidative stress colored red while proteins whose synthesis was switched off by the stress factor colored green. Proteins that were continuously synthesized before and after the imposition of stress retained their yellow color. The advantages and possible pitfalls of the technique are discussed.

The amphipathic helix concept: length effects on ideally amphipathic LiKj(i=2j) peptides to acquire optimal hemolytic activity

In a minimalist approach to modeling lytic toxins, amphipathic peptides of LiKj with i=2j composition and whose length varies from 5 to 22 residues were studied for their ability to induce hemolysis and lipid vesicle leakage. Their sequences were designed to generate ideally amphipathic alpha helices with a single K residue per putative turn. All the peptides were lytic, their activities varying by more than a factor of 103 from the shortest 5-residue-long peptide (5-mer) to the longest 22-mer. However, there was no monotonous increase versus length. The 15-mer was as active as the 22-mer and even more than melittin which is used as standard. Partition coefficients from the buffer to the membrane increased in relation to length up to 12 residues, then weakly decreased to reach a plateau, while they were expected to increase monotonously with peptide length and hydrophobicity as revealed from HPLC retention times. Fluorescence labeling by a dansyl group at the N-terminus, or by a W near the CO-terminus, show that up to 12 residues, the peptides were essentially monomeric while longer peptides strongly aggregated in the solution. Lipid affinity was then controlled by peptide length and was found to be limited by folding and self-association in buffer. The lytic activity resulted both from lipid affinity, which varied by a factor of 20-fold, and from efficiency in disturbing the membrane when bound, the latter steeply and monotonously increasing with length. The 15-residue-long peptide, KLLKLLLKLLLKLLK, had the optimal size for highest lytic activity. The shallow location of the fluorescent labels in the lipids is further evidence for a model of peptides remaining flat at the interface.

[Preoperative diagnosis in laparoscopic cholecystectomy: is intravenous cholangiography currently still justified?]

Laparocopic cholecystectomy requires essentially the safe exclusion of choledocholithias. The aim of this study was to compare the intravenous cholangiography and ERCP in addition to a basic program (case history, laboratory results ultrasound) with references to the diagnostic ability and therapeutic consequences in patients with choledocholithiasis. The results show, that the intravenous cholangiography not provides extra important informations after the case history, ultrasound and laboratory findings and therefore its general use is not justified. Instead of the intravenous cholangiography the preoperative ERCP should be performed generously if choledocholithiasis is suspected, especially because the ERCP offers the possibility to extract the stone.

Copurification of ribosomal protein S2 and DNA-dependent RNA polymerase from heat-shocked cells of Bacillus subtilis

The DNA-dependent RNA polymerases from heat-shocked and vegetatively grown cells of Bacillus subtilis were isolated and compared. The RNA polymerase from non-stressed cells had the well known alpha, beta, beta' and sigma composition of eubacterial RNA polymerases. The RNA polymerase from heat-shocked cells exhibited one additional band shown by SDS-PAGE. N-terminal sequencing of the first 16 amino acids of the associated protein demonstrated its identity with the ribosomal protein S2.

Urinary levels of 1-hydroxypyrene, 1-, 2-, 3-, and 4-hydroxyphenanthrene in females living in an industrial area of Germany

The concentrations of 1-hydroxypyrene (1-HOPYR), and 1-, 2-, 3-, and 4-hydroxyphenanthrene (HOPHE) as metabolites of pyrene and phenanthrene, were measured in urine samples collected from 124 housewives (27 smokers and 97 non-smokers) living in Bottrop, an industrial city located in the Ruhr area in Germany. The urine samples were analyzed by a very sensitive and practical high-performance liquid chromatographic (HPLC) method using a two-column switching technique and a special precolumn packing material followed by fluorescence detection. The polycyclic aromatic hydrocarbon (PAH) metabolites are selectively enrichéd on the precolumn and separated from the matrix. Therefore, laborious clean-up steps were omitted. The above-mentioned PAH metabolites could be detected in all urine samples investigated. Smokers had significantly higher urine concentrations of 1-HOPYR (median 0.48 microgram/g creatinine), 3-HOPHE (median 0.61 microgram/g creatinine), 2-HOPHE (0.41 microgram/g creatinine) and 4-HOPHE (median 0.10 microgram/g creatinine) than non-smokers (median 0.15 microgram/g creatinine, 0.31 microgram/g creatinine, 0.31 microgram/g creatinine and 0.04 microgram/g creatinine, respectively). The study shows that the influence of smoking is of such an order of magnitude that potential environmental exposure to PAH in this highly industrialized area is obscured by smoking habits. Furthermore, it can be concluded that the determination of 1-HOPYR, 1-, 2-, 3-, and 4-HOPHE in urine is a diagnostically useful method for the biological monitoring of persons environmentally exposed to PAH.

The amphipathic alpha-helix concept. Application to the de novo design of ideally amphipathic Leu, Lys peptides with hemolytic activity higher than that of melittin

An original series of 12- to 22-residue-long peptides was developed, they are only constituted by apolar Leu and charged Lys residues periodically located in the sequence in order to general ideal highly amphipathic alpha-helices. By circular dichroism, the peptides are proven to be mainly alpha-helical in organic and aqueous solvents and in the presence of lipids. The peptides are highly hemolytic, their activity varies according to the peptide length. The 15-, 20-, and 22-residue-long-peptides have LD50 approximately 5 x 10(-8) M for 10(7) erythrocytes, i.e. they are 5-10 times more active than melittin, and are indeed several orders of magnitude more active than magainin or mastoparan.

Evaluation of peptide-peptide interactions using reversed-phase high-performance liquid chromatography

The separation of peptides during RP-HPLC depends mainly upon differential hydrophobic interactions of the individual peptides being separated with the C18 group of the stationary phase. We have examined the behavior of dimeric disulfide-linked model peptides during RP-HPLC in order to study self-induced conformational effects. A set of 18 analogues of the amphipathic alpha-helical sequence Ac-LKLLKKLLKKLKKLLKKL-NH2 was used for this study. These analogues differed only by the successive replacement of each position with a cysteine. Strong peptide-peptide interactions, occurring through interchain hydrophobic forces, resulted in a presenting face to the C18 group, consisting primarily of lysine residues and, in turn, in early retention times. Three homo-dimers were also found to be strongly alpha-helical in water as determined by circular dichroism spectroscopy.

Anomalous reversed-phase high-performance liquid chromatographic behavior of synthetic peptides related to antigenic helper T cell sites

Sets of overlapping synthetic peptides for three well characterized proteins (sperm whale myoglobin, hen egg lysozyme, and the circumsporozoite protein from Plasmodium falciparum) were prepared and examined by reversed-phase high-performance liquid chromatography (RP-HPLC). Using retention coefficients to predict the retention time of each peptide, several peptides in each protein set were found that exhibited anomalous behavior (i.e. eluted significantly later than predicted). Previous work with model peptides has shown that this anomalous behavior can be attributed to specific amphipathic arrangements induced by the lipid stationary phase during the RP-HPLC process. In the current study it was found that although not all of the peptides containing an antigenic T cell site displayed anomalously late behavior, all of the peptides which eluted anomalously late during RP-HPLC included the regions of these proteins known from earlier studies to be antigenic T cell sites.