In silico analysis of the 16S rRNA gene of endophytic bacteria, isolated from the aerial parts and seeds of important agricultural crops.

Because of human population growth, increased food production and alternatives to conventional methods of biocontrol and development of plants such as the use of endophytic bacteria and fungi are required. One of the methods used to study microorganism diversity is sequencing of the 16S rRNA gene, which has several advantages, including universality, size, and availability of databases for comparison. The objective of this study was to analyze endophytic bacterial diversity in agricultural crops using published papers, sequence databases, and phylogenetic analysis. Fourteen papers were selected in which the ribosomal 16S rRNA gene was used to identify endophytic bacteria, in important agricultural crops, such as coffee, sugar cane, beans, corn, soybean, tomatoes, and grapes, located in different geographical regions (America, Europe, and Asia). The corresponding 16S rRNA gene sequences were selected from the NCBI database, aligned using the Mega 5.2 program, and phylogenetic analysis was undertaken. The most common orders present in the analyzed cultures were Bacillales, Enterobacteriales, and Actinomycetales and the most frequently observed genera were Bacillus, Pseudomonas, and Microbacterium. Phylogenetic analysis showed that only approximately 1.56% of the total sequences were not properly grouped, demonstrating reliability in the identification of microorganisms. This study identified the main genera found in endophytic bacterial cultures from plants, providing data for future studies on improving plant agriculture, biotechnology, endophytic bacterium prospecting, and to help understand relationships between endophytic bacteria and their interactions with plants.

Proteolysis of surfactant protein D by cystic fibrosis relevant proteases.

Surfactant protein D (SP-D) is an important innate host defense molecule that has been shown to interact with cystic fibrosis (CF)-associated pathogens. Previous studies demonstrated that rat SP-D is highly resistant to degradation by a wide range of proteolytic enzymes. The aim of this study was to examine whether human SP-D can be degraded by CF relevant proteases ex vivo and in vitro. Bronchoalveolar lavage fluids (BALFs) of 11 patients with CF in a stable clinical condition were examined for SP-D by immunoblotting. In vitro, purified human SP-D was treated with human leukocyte elastase, proteinase 3, cathepsin G or Pseudomonas elastase followed by immunoblotting with specific antibodies to SP-D. In BALF of 8 of the 11 patients investigated, proteolytic fragments or absence of SP-D were detected. In vitro proteolysis of SP-D was observed in a time-dependent manner for each protease applied. The presence of Ca(++) at a physiologic concentration delayed, but did not prevent the degradation. We conclude that SP-D is an important target of numerous proteases present in the CF lung. Host defense is probably impaired due to proteolysis of SP-D and may contribute to the suppurative lung disease in CF.

Surfactant protein A and other bronchoalveolar lavage fluid proteins are altered in cystic fibrosis.

Inflammation and proteolytic processes play an important role in the progression of cystic fibrosis (CF) lung disease. The goal of this study was to describe bronchoalveolar lavage fluid (BALF) protein pattern of CF patients in comparison to controls and to assess if there is proteolytic degradation of surfactant protein A (SP-A), an important innate host defence component of the lungs. BALFs from 17 clinically stable CF patients and from eight healthy children were separated by two-dimensional gel electrophoresis. Silver staining was used to show BALF proteins and Western blotting to detect SP-A isoforms. In CF, BALF proteins of a low molecular weight < or = 20 kD were more abundant than in controls. Various proteins were seen in CF which were not present in controls and vice versa. Degradation of SP-A was present in 15 of 17 CF BALFs but in none of the controls, in contrast polymeric isoforms were seen in all controls and in four of 17 CF patients. Proteolytic damage to surfactant protein A and significant changes of normal bronchoalveolar lavage fluid proteins occur in lungs of cystic fibrosis patients. Identification of altered bronchoalveolar lavage fluid proteins may give new insights into pathogenic mechanisms and provide new targets for therapy.

Reduced proteolysis of surfactant protein A and changes of the bronchoalveolar lavage fluid proteome by inhaled alpha 1-protease inhibitor in cystic fibrosis.

In cystic fibrosis (CF), the chronic neutrophilic inflammation of the airways results in proteolytic degradation of lung tissue early in the course of the disease. Inhalation of alpha 1-protease inhibitor (alpha 1-PI) may restore the protease-antiprotease imbalance and thus lead to less tissue damage. To monitor its impacts on bronchoalveolar lavage (BAL) fluid protein pattern (proteome) and on surfactant protein A (SP-A), eight young adults with CF inhaled 100 mg of alpha 1-PI twice daily over eight weeks. BAL fluids were obtained before and after inhalation. Total protein, the number and amount of proteins with a molecular mass < 20 kDa were reduced compared to pretreatment values. Degradation products of SP-A were shown by immunoblotting, being reduced after alpha 1-PI treatment. This pilot study demonstrates that inhalation of alpha 1-PI is associated with biochemical changes consistent with reduced proteolysis. The display of the BAL proteome by two-dimensional electrophoresis may be helpful to quantify the overall molecular changes associated with proteolytic or other lung injuries and offers the possibility to monitor directly therapeutic interventions.

Inhalation of alpha(1)-protease inhibitor in cystic fibrosis does not affect surfactant convertase and surface activity.

The inhalation of alpha(1)-protease inhibitor (alpha(1)-PI) was assessed in a pilot study to restore the protease-antiprotease balance in the lungs of cystic fibrosis (CF) patients. In addition, the effect of this treatment on the surface active properties of lung surfactant and the metabolic conversion of aggregate forms was studied. Eight young adults with CF inhaled 100 mg of alpha(1)-PI twice daily over 8 weeks and bronchoalveolar lavages (BAL) were obtained before and 12 h after the last inhalation. Large aggregate (LA) forms of surfactant were isolated from the in vivo material by ultracentrifugation and their conversion into small aggregates (SA) was assessed by an in vitro surface area cycling assay. Although alpha(1)-PI partially restored the protease-anti-protease imbalance and reduced BAL protein content, no effects were noted on the impaired minimal surface tension and on the in vivo and in vitro conversion of LA to SA. Antiserum against the specific carboxyl esterase ES-2, previously identified in mice and rats as the putative surfactant convertase, did not detect a protein of the appropriate size in CF BAL. Whereas short-term inhalation of alpha(1)-PI was beneficial for the proteolytic aspects of CF lung injury, this appeared not to be the case for surfactant conversion and surface activity.