Non-pathogenic Soil Bacterium Research Articles

Structural characterization and antioxidant activity of an extracellular polysaccharide isolated from Brevibacterium otitidis BTS 44

A water-soluble acidic extracellular polysaccharide reaching a maximum concentration of 23.4 g/l growth medium, coded as BSMA, was isolated from the non-pathogenic soil bacteria Brevibacterium otitidis BTS44, by precipitating with two volumes of ethanol. BSMA consisted of arabinose, mannose, glucose and mannouronic acid in ratios of 2.7:3.6:2.1:1.0. No protein was detected in the BSMA fraction, and its molecular weight was about 127 kDa. It has a backbone composed of (1 → 5)-linked arabinose, (1 → 6)-linked mannose with three branches attached to O-3 of (1 → 6)-linked mannose and terminated with either mannose, or mannose and glucose; all the glucose and most of the mannouronic acid are distributed in branches. Partial acid hydrolysis of BSMA gave four sub-fractions termed BSMA-1, BSMA-2, BSMA-3 and BSMA-4. BSMA-1 was composed of arabinose, mannose and trace amounts of mannouronic acid; BSMA-2 was only composed of arabinose and mannose; BSMA-3 was composed of mannose, mannouronic acid and glucose, and BSMA-4 was only composed of mannose and glucose. In the in vitro antioxidant assay, BSMA was found to possess DPPH radical-scavenging activity, with an IC 50 value of 120 μg/ml.

Cell wall proteome analysis of Mycobacterium smegmatis strain MC2 155

BackgroundThe usually non-pathogenic soil bacterium Mycobacterium smegmatis is commonly used as a model mycobacterial organism because it is fast growing and shares many features with pathogenic mycobacteria. Proteomic studies of M. smegmatis can shed light on mechanisms of mycobacterial growth, complex lipid metabolism, interactions with the bacterial environment and provide a tractable system for antimycobacterial drug development. The cell wall proteins are particularly interesting in this respect. The aim of this study was to construct a reference protein map for these proteins in M. smegmatis.ResultsA proteomic analysis approach, based on one dimensional polyacrylamide gel electrophoresis and LC-MS/MS, was used to identify and characterize the cell wall associated proteins of M. smegmatis. An enzymatic cell surface shaving method was used to determine the surface-exposed proteins. As a result, a total of 390 cell wall proteins and 63 surface-exposed proteins were identified. Further analysis of the 390 cell wall proteins provided the theoretical molecular mass and pI distributions and determined that 26 proteins are shared with the surface-exposed proteome. Detailed information about functional classification, signal peptides and number of transmembrane domains are given next to discussing the identified transcriptional regulators, transport proteins and the proteins involved in lipid metabolism and cell division.ConclusionIn short, a comprehensive profile of the M. smegmatis cell wall subproteome is reported. The current research may help the identification of some valuable vaccine and drug target candidates and provide foundation for the future design of preventive, diagnostic, and therapeutic strategies against mycobacterial diseases.

Mycobacterial Cytochrome P450 125 (Cyp125) Catalyzes the Terminal Hydroxylation of C27 Steroids

Cyp125 (Rv3545c), a cytochrome P450, is encoded as part of the cholesterol degradation gene cluster conserved among members of the Mycobacterium tuberculosis complex. This enzyme has been implicated in mycobacterial pathogenesis, and a homologue initiates cholesterol catabolism in the soil actinomycete Rhodococcus jostii RHA1. In Mycobacterium bovis BCG, cyp125 was up-regulated 7.1-fold with growth on cholesterol. A cyp125 deletion mutant of BCG did not grow on cholesterol and accumulated 4-cholesten-3-one when incubated in the presence of cholesterol. Wild-type BCG grew on this metabolite. By contrast, a parallel cyp125 deletion mutation of M. tuberculosis H37Rv did not affect growth on cholesterol. Purified Cyp125 from M. tuberculosis, heterologously produced in R. jostii RHA1, bound cholesterol and 4-cholesten-3-one with apparent dissociation constants of 0.20 +/- 0.02 microM and 0.27 +/- 0.05 microm, respectively. When reconstituted with KshB, the cognate reductase of the ketosteroid 9alpha-hydroxylase, Cyp125 catalyzed the hydroxylation of these steroids. MS and NMR analyses revealed that hydroxylation occurred at carbon 26 of the steroid side chain, allowing unambiguous classification of Cyp125 as a steroid C26-hydroxylase. This study establishes the catalytic function of Cyp125 and, in identifying an important difference in the catabolic potential of M. bovis and M. tuberculosis, suggests that Cyp125 may have an additional function in pathogenesis.

Key Residues in Mycobacterium tuberculosis Protein Kinase G Play a Role in Regulating Kinase Activity and Survival in the Host

Protein kinase G (PknG) in Mycobacterium tuberculosis has been shown to modulate phagosome-lysosome fusion. The protein has three distinct domains, an N-terminal Trx domain, a kinase domain, and a C-terminal TPR domain. The present study extensively analyzes the roles of these domains in regulating PknG kinase activity and function. We find that the kinase domain of PknG by itself is inactive, signifying the importance of the flanking domains. Although the deletion of the Trx domain severely impacts the activity of the protein, the C-terminal region also contributes significantly in regulating the activity of the kinase. Apart from this, PknG kinase activity is dependent on the presence of threonine 309 in the p + 1 loop of the activation segment. Mutating the conserved cysteine residues in the Trx motifs makes PknG refractory to changes in the redox environment. In vitro experiments identify threonine 63 as the major phosphorylation site of the protein. Importantly, we find that this is the only site in the protein that is phosphorylated in vivo. Macrophage infection studies reveal that the first 73 residues, the Trx motifs, and the threonine 63 residue are independently essential for modulating PknG-mediated survival of mycobacteria in its host. We have extended these studies to investigate the role of PknG and PknG mutants in the pathogenesis of mycobacteria in mice. Our results reinforce the findings from the macrophage infection experiments, and for the first time demonstrate that the expression of PknG in non-pathogenic mycobacteria allows the continued existence of these bacteria in host tissues.

TheAcinetobacter baylyi hfqGene Encodes a Large Protein with an Unusual C Terminus

In gammaproteobacteria the Hfq protein shows a great variation in size, especially in its C-terminal part. Extremely large Hfq proteins consisting of almost 200 amino acid residues and more are found within the gammaproteobacterial family Moraxellaceae. The difference in size compared to other Hfq proteins is due to a glycine-rich domain near the C-terminal end of the protein. Acinetobacter baylyi, a nonpathogenic soil bacterium and member of the Moraxellaceae encodes a large 174-amino-acid Hfq homologue containing the unique and repetitive amino acid pattern GGGFGGQ within the glycine-rich domain. Despite the presence of the C-terminal extension, A. baylyi Hfq complemented an Escherichia coli hfq mutant in vivo. By using polyclonal anti-Hfq antibodies, we detected the large A. baylyi Hfq that corresponds to its annotated size indicating the expression and stability of the full protein. Deletion of the complete A. baylyi hfq open reading frame resulted in severe reduction of growth. In addition, a deletion or overexpression of Hfq was accompanied by the loss of cell chain assembly. The glycine-rich domain was not responsible for growth and cell phenotypes. hfq gene localization in A. baylyi is strictly conserved within the mutL-miaA-hfq operon, and we show that hfq expression starts within the preceding miaA gene or further upstream.

Multicellular behaviour and production of a wide variety of toxic substances support usage of Bacillus subtilis as a powerful biocontrol agent.

Intensive cultivation of plants in the monoculture field system in order to feed the continuously growing human population creates a need for their protection from the variety of natural competitors such as: bacteria, fungi, insects as well as other plants. The increase in the use of chemical substances in the 20th century has brought many effective solutions for the agriculture. However, it was extremely difficult to obtain a substance, which would be directed solely against a specific plant pathogen and would not be harmful for the environment. In the late 1900's scientists began trying to use natural antagonisms between resident soil organism to protect plants. This phenomenon was named biocontrol. Biological control of plants by microorganisms is a very promising alternative to an extended use of pesticides, which are often expensive and accumulate in plants or soil, having adverse effects on humans. Nonpathogenic soil bacteria living in association with roots of higher plants enhance their adaptive potential and, moreover, they can be beneficial for their growth. Here, we present the current status of the use of Bacillus subtilis in biocontrol. This prevalent inhabitant of soil is widely recognized as a powerful biocontrol agent. Naturally present in the immediate vicinity of plant roots, B. subtilis is able to maintain stable contact with higher plants and promote their growth. In addition, due to its broad host range, its ability to form endospores and produce different biologically active compounds with a broad spectrum of activity, B. subtilis as well as other Bacilli are potentially useful as biocontrol agents.

The Crystal Structure of Mismatch-specific Uracil-DNA Glycosylase (MUG) from Deinococcus radiodurans Reveals a Novel Catalytic Residue and Broad Substrate Specificity

Deinococcus radiodurans is extremely resistant to the effects of ionizing radiation. The source of the radiation resistance is not known, but an expansion of specific protein families related to stress response and damage control has been observed. DNA repair enzymes are among the expanded protein families in D. radiodurans, and genes encoding five different uracil-DNA glycosylases are identified in the genome. Here we report the three-dimensional structure of the mismatch-specific uracil-DNA glycosylase (MUG) from D. radiodurans (drMUG) to a resolution of 1.75 angstroms. Structural analyses suggest that drMUG possesses a novel catalytic residue, Asp-93. Activity measurements show that drMUG has a modified and broadened substrate specificity compared with Escherichia coli MUG. The importance of Asp-93 for activity was confirmed by structural analysis and abolished activity for the mutant drMUGD93A. Two other microorganisms, Bradyrhizobium japonicum and Rhodopseudomonas palustris, possess genes that encode MUGs with the highest sequence identity to drMUG among all of the bacterial MUGs examined. A phylogenetic analysis indicates that these three MUGs form a new MUG/thymidine-DNA glycosylase subfamily, here called the MUG2 family. We suggest that the novel catalytic residue (Asp-93) has evolved to provide drMUG with broad substrate specificity to increase the DNA repair repertoire of D. radiodurans.

Mass spectrometry of the M. smegmatis proteome: Protein expression levels correlate with function, operons, and codon bias

The fast-growing bacterium Mycobacterium smegmatis is a model mycobacterial system, a nonpathogenic soil bacterium that nonetheless shares many features with the pathogenic Mycobacterium tuberculosis, the causative agent of tuberculosis. The study of M. smegmatis is expected to shed light on mechanisms of mycobacterial growth and complex lipid metabolism, and provides a tractable system for antimycobacterial drug development. Although the M. smegmatis genome sequence is not yet completed, we used multidimensional chromatography and tandem mass spectrometry, in combination with the partially completed genome sequence, to detect and identify a total of 901 distinct proteins from M. smegmatis over the course of 25 growth conditions, providing experimental annotation for many predicted genes with an approximately 5% false-positive identification rate. We observed numerous proteins involved in energy production (9.8% of expressed proteins), protein translation (8.7%), and lipid biosynthesis (5.4%); 33% of the 901 proteins are of unknown function. Protein expression levels were estimated from the number of observations of each protein, allowing measurement of differential expression of complete operons, and the comparison of the stationary and exponential phase proteomes. Expression levels are correlated with proteins' codon biases and mRNA expression levels, as measured by comparison with codon adaptation indices, principle component analysis of codon frequencies, and DNA microarray data. This observation is consistent with notions that either (1) prokaryotic protein expression levels are largely preset by codon choice, or (2) codon choice is optimized for consistency with average expression levels regardless of the mechanism of regulating expression.

Extracellular polysaccharides production by Arthrobacter viscosus

In this study the production of extracellular polysaccharides by the non-pathogenic soil bacteria Arthrobacter viscosus has been investigated. Different variables affecting extracellular polysaccharide production such as the carbon source (glucose or xylose), the agitation speed and the pH have been analysed. In a first stage, experiments in shaken conical flasks (250 ml), containing 50 ml of culture medium, were carried out. Using xylose (25 g/l) as the carbon source at an initial pH 8 improved the extracellular polysaccharides levels obtained. In a second stage, the experiments were scaling in bioreactors. Cultivation was carried out in discontinuous mode and with/without pH control. Polysaccharide production reached a maximum of 10 g of crude product per litre of growth medium after 14 days and the relationship between product formation and cell growth of A. viscosus is 2.7 g polysaccharide per gram biomass. This production was obtained at the optimal conditions determined with pH control at pH 7, xylose as carbon source (25 g/l) and an agitation rate of 800 rpm.

Preparation, characterization and biological activity of Schiff base compounds derived from 8-hydroxyquinoline-2-carboxaldehyde and Jeffamines ED ®

Polyethers with 8-hydroxyquinolin-2-yl end groups (HOQCHN–POE–NCHQOH) were prepared by reaction between polyethers having amino end groups (Jeffamines ED ®) and 8-hydroxyquinoline-2-carboxaldehyde. The HOQCHN–POE–NCHQOH polymers were characterized by size-exclusion chromatography, UV, IR, 1 H and 13 C NMR spectroscopy, and MALDI-TOF mass spectrometry. The complexation between HOQCHN–POE–NCHQOH and Fe 3+ was studied by UV, IR spectroscopy and differential scanning calorimetry. The UV-irradiation of the complexes caused photodegradation of the polyether chains. It was shown that HOQCHN–POE–NCHQOH had high efficacy on remedying iron-deficient maize plants and exhibited very low-antibacterial activity towards non-pathogenic soil bacteria ( B. subtilis).

Identification and Mutational Analysis ofrfbG,the Gene Encoding CDP-D-Glucose-4,6-Dehydratase, Isolated from Free Living Soil BacteriumAzotobacter vinelandii

We have identified therfbGfrom a non-symbiotic and non-pathogenic soil bacterium,Azotobacter vinelandii.The nucleotide sequence analysis of therfbGrevealed an open reading frame that encodes a peptide of 360 amino acids. This deduced peptide shares 57% homology with the RfbG ofSynechocystisand 47% homology with the RfbG ofYersinia pseudotuberculosis.The previously identified short-chain dehydrogenases/reductases family signature sequence is conserved in the sequence of the RfbG ofA. vinelandii.Southern blotting analysis ofA. vinelandiichromosome by probed with 1.1kbPstI DNA fragment corresponding torfbGrevealed that it is present as single copy onA. vinelandiichromosome. Disrupting therfbGpresent on the chromosome ofA. vinelandii,by insertion of kanamycin resistance marker via homologous recombination, resulted in drastic changes in the growth characteristics. TherfbG-negativeA. vinelandiigrown in liquid medium exhibited agglutination that is characteristic ofrfb−mutants of other bacteria, suggesting that we have cloned the functional copy of therfbGofA. vinelandii.

The three domains of a bacterial sialidase: a beta-propeller, an immunoglobulin module and a galactose-binding jelly-roll.

Sialidases, or neuraminidases, have been implicated in the pathogenesis of many diseases, but are also produced by many non-pathogenic bacteria. Bacterial sialidases are very variable in size, often possessing domains in addition to the catalytic domain. The sialidase from the non-pathogenic soil bacterium Micromonospora viridifaciens is secreted in two forms with molecular weights of 41 kDa or 68 kDa, depending on the nature of the carbohydrate used to induce expression. We report here the X-ray crystal structures of the 41 kDa and 68 kDa forms of the sialidase from M. viridifaciens at 1.8 A and 2.5 A resolution respectively. In addition, we report a complex of the 41 kDa form with an inhibitor at 2.0 A resolution, and a complex of the 68 kDa form with galactose at 2.5 A. The 41 kDa form shows the canonical sialidase beta-propeller fold. The 68 kDa form possesses two additional domains, one with an immunoglobulin-like fold that serves as a linker to the second, which is homologous to the galactose-binding domain of a fungal galactose oxidase. The presence of the additional carbohydrate-binding domain in the 68 kDa form of the bacterial sialidase reported here is a further example of a combination of carbohydrate binding and cleaving domains which we observed in the sialidase from Vibrio cholerae. This dual function may be common, but only to other bacterial and parasitic sialidases, but also to other secreted glycosidases involved in pathogenesis. The bacterium may have acquired both the immunoglobulin module and the galactose-binding module from eukaryotes, as the enzyme shows a remarkable similarity to a fungal galactose oxidase which possesses similar domains performing different functions and assembled in a different order.