Protein sequences insight into heavy metal tolerance in Cronobacter sakazakii BAA-894 encoded by plasmid pESA3

Isolation, screening, and characterization of heavy metal-resistant bacteria from solid waste dumping sites in Central Gondar, Northwest, Ethiopia

OBJECTIVE

Heavy metal pollution is one of the more recent problems of environmental degradation caused by rapid industrialization and human activity. The objective of this study was to isolate, screen, and characterize heavy metal-resistant bacteria from solid waste disposal sites.

METHODS

In this study, a total of 18 soil samples were randomly selected from mechanical sites, metal workshops, and agricultural land that received wastewater irrigation. Isolation and screening of the isolates were based on multiple heavy metal (copper (Cu), chromium (Cr), and lead (Pb)) resistance potential. Morphological, biochemical, and 16S rRNA gene sequencing techniques were used to identify the isolates. The minimum inhibitory concentration (MIC) of the potential isolates was further examined at various concentrations (3, 6, 12, 25, 50, and 100 µg/mL). Each isolate's ability to biodegrade and resist antibiotics was also examined.

RESULTS

About 21 bacterial isolates were obtained. Among these, six potential isolates (Agri10-2Is2, Agri10-3Is2, Agri10-3Is1, AL10-1Is2, AL10-3Is1, and GA10-2Is1) were selected. The isolates displayed varied colony morphologies and biochemical characterization features. Phylogenetic tree results revealed that Agri10-2Is2, Agri10-3Is2, Agri10-3Is1, AL10-1Is2, AL10-3Is1, and GA10-2Is1 were identified as Bacillus subtilis, Bacillus subtilis, Bacillus species, Bacillus tequilensis, Klebiesella species, and Cronobacter sakazakii, respectively. Every isolate gave a different MIC value. The biodegradation capacity of Agri10-2Is2, Agri10-3Is2, Agri10-3Is1, AL10-1Is2, AL10-3Is1, and GA10-2Is1 was 92.2%, 92.57%, 92.37%, 92.66%, 92.85%, and 92.52% against Cu; 95.07%, 94.07%, 93.07%, 93.4%, 91.4%, and 94.4% on Cr; and 95.51%, 94.53%, 95.62%, 96.87%, 94.86%, and 97.09% against Pb, respectively. All isolates were found to be resistant to the tested antibiotics.

CONCLUSION

This study concludes that the selected bacterial isolates could be potential agents for bioremediation of heavy metal-polluted environments.

Modified lignocellulose and rich starch for complete saccharification to maximize bioethanol in distinct polyploidy potato straw

Potato is a major food crop with enormous biomass straw, but lignocellulose recalcitrance causes a costly bioethanol conversion. Here, we selected the cytochimera (Cyt) potato samples showing significantly-modified lignocellulose and much increased soluble sugars and starch by 2-4 folds in mature straws. Under two pretreatments (8 min liquid hot water; 5% CaO) at minimized conditions, the potato Cyt straw showed complete enzymatic saccharification. Further performing yeast fermentation with all hexoses released from soluble sugars, starch and lignocellulose in the Cyt straw, this study achieved a maximum bioethanol yield of 24 % (% dry matter), being higher than those of other bioenergy crops as previously reported. Hence, this study has proposed a novel mechanism model on the reduction of major lignocellulose recalcitrance and regulation of carbon assimilation to achieve cost-effective bioethanol production under optimal pretreatments. This work also provides a sustainable strategy for utilization of potato straws with minimum waste release.

Understanding Calcium-Dependent Conformational Changes in S100A1 Protein: A Combination of Molecular Dynamics and Gene Expression Study in Skeletal Muscle

The S100A1 protein, involved in various physiological activities through the binding of calcium ions (Ca2+), participates in several protein-protein interaction (PPI) events after Ca2+-dependent activation. The present work investigates Ca2+-dependent conformational changes in the helix-EF hand-helix using the molecular dynamics (MD) simulation approach that facilitates the understanding of Ca2+-dependent structural and dynamic distinctions between the apo and holo forms of the protein. Furthermore, the process of ion binding by inserting Ca2+ into the bulk of the apo structure was simulated by molecular dynamics. Expectations of the simulation were demonstrated using cluster analysis and a variety of structural metrics, such as interhelical angle estimation, solvent accessible surface area, hydrogen bond analysis, and contact analysis. Ca2+ triggered a rise in the interhelical angles of S100A1 on the binding site and solvent accessible surface area. Significant configurational regulations were observed in the holo protein. The findings would contribute to understanding the molecular basis of the association of Ca2+ with the S100A1 protein, which may be an appropriate study to understand the Ca2+-mediated conformational changes in the protein target. In addition, we investigated the expression profile of S100A1 in myoblast differentiation and muscle regeneration. These data showed that S100A1 is expressed in skeletal muscles. However, the expression decreases with time during the process of myoblast differentiation.

Transcriptome-wide analysis reveals the progress of Cordyceps militaris subculture degeneration

BACKGROUND

The entomopathogenic mushroom Cordyceps militaris is an important medicinal and food resource owing to its various medicinal components and pharmacological effects. However, the high frequency of strain degeneration during subculture seriously restricts the large-scale production of C. militaris, and the mechanism underlying strain degeneration remains unclear. In this study, we artificially cultured C. militaris for six generations and compared changes during fruiting body growth. The transcriptome of six generations of C. militaris strains were sequenced with the Illumine Hiseq4000.

RESULTS

The subcultured C. militaris strains degenerated beginning at the third generation, with incomplete fruiting body growth beginning at the fourth generation. Over 9,015 unigenes and 731 new genes were identified. In addition, 35,323 alternative splicing (AS) events were detected in all samples, and more AS events occurred in the second, fourth and sixth generations. Compared with the first generation, the third generation (degenerated strain) included 2,498 differentially expressed genes (DEGs) including 1,729 up-regulated and 769 down-regulated genes. This number was higher than the number of DEGs in the second (1,892 DEGs), fourth (2,006 DEGs), fifth (2,273 DEGs) and sixth (2,188 DEGs) generations. Validation of RNA-seq by qRT-PCR showed that the expression patterns of 51 DEGs were in accordance with the transcriptome data.

CONCLUSION

Our results suggest that the mechanism of C. militaris strain degeneration is associated with gene involved in toxin biosynthesis, energy metabolism, and DNA methylation and chromosome remodeling.

DNA-Sequence Based Typing of the Cronobacter Genus Using MLST, CRISPR-cas Array and Capsular Profiling

The Cronobacter genus is composed of seven species, within which a number of pathovars have been described. The most notable infections by Cronobacter spp. are of infants through the consumption of contaminated infant formula. The description of the genus has greatly improved in recent years through DNA sequencing techniques, and this has led to a robust means of identification. However some species are highly clonal and this limits the ability to discriminate between unrelated strains by some methods of genotyping. This article updates the application of three genotyping methods across the Cronobacter genus. The three genotyping methods were multilocus sequence typing (MLST), capsular profiling of the K-antigen and colanic acid (CA) biosynthesis regions, and CRISPR-cas array profiling. A total of 1654 MLST profiled and 286 whole genome sequenced strains, available by open access at the PubMLST Cronobacter database, were used this analysis. The predominance of C. sakazakii and C. malonaticus in clinical infections was confirmed. The majority of clinical strains being in the C. sakazakii clonal complexes (CC) 1 and 4, sequence types (ST) 8 and 12 and C. malonaticus ST7. The capsular profile K2:CA2, previously proposed as being strongly associated with C. sakazakii and C. malonaticus isolates from severe neonatal infections, was also found in C. turicensis, C. dublinensis and C. universalis. The majority of CRISPR-cas types across the genus was the I-E (Ecoli) type. Some strains of C. dublinensis and C. muytjensii encoded the I-F (Ypseudo) type, and others lacked the cas gene loci. The significance of the expanding profiling will be of benefit to researchers as well as governmental and industrial risk assessors.