scholarly journals Genomic and Transcriptome Analyses of a Thermophilic Bacterium Geobacillus stearothermophilus B5 Isolated from Compost Reveal Its Enzymatic Basis for Lignocellulose Degradation

2020 ◽  
Vol 8 (9) ◽  
pp. 1357
Author(s):  
Mengmeng Wang ◽  
Jiaxi Miao ◽  
Xuanqing Wang ◽  
Tuo Li ◽  
Han Zhu ◽  
...  
Keyword(s):  
Thermophilic Bacterium ◽  
Glycoside Hydrolases ◽  
Lignocellulose Degradation ◽  
Geobacillus Stearothermophilus ◽  
Carbohydrate Active Enzymes ◽  
Transcriptional Responses ◽  
Protein Coding ◽  
Clusters Of Orthologous Groups ◽  
Different Temperatures ◽  
Shock Proteins

A lignocellulose-degrading strain isolated from thermophilic compost was identified as Geobacillus stearothermophilus B5, and found able to secrete considerable amounts of enzymes at optimal temperature (60 °C) and pH (7.5). One circular contig of 3.37 Mbp was assembled from raw data, and 3371 protein-coding genes were predicted. Clusters of orthologous groups (COG) analysis revealed various genes with functions in polymeric substrate degradation, especially for Carbohydrate Active enZymes (CAZymes), such as glycoside hydrolases (GHs) and glycosyl transferases (GTs). Furthermore, the transcriptional responses of B5 at different temperatures—with rice straw provided as the sole carbon source—were analyzed. The results revealed that B5 could resist high temperature by upregulating heat shock proteins (HSPs), enhancing protein synthesis, and decreasing carbon catabolism. Briefly, B5 possesses the ability of lignocellulose degradation, and might be considered a potential inoculant for improving composting efficiency.

scholarly journals Genomic and transcriptome analyses of a thermophilic bacterium Geobacillus stearothermophilus B5 isolated from compost reveal its enzymatic basis for lignocellulose degradation

2020 ◽  
Author(s):  
Mengmeng Wang ◽  
Jiaxi Miao ◽  
Xuanqing Wang ◽  
Tuo Li ◽  
Han Zhu ◽  
...  
Keyword(s):  
Cellulose Degradation ◽  
Carbon Sources ◽  
Thermophilic Bacterium ◽  
Glycoside Hydrolases ◽  
Lignocellulose Degradation ◽  
Geobacillus Stearothermophilus ◽  
Transcriptional Responses ◽  
Protein Coding ◽  
Thermophilic Microorganisms ◽  
Clusters Of Orthologous Groups

Abstract Background Composting is a special global carbon cycle which sustains various microbes engendering the cellulose degradation. Studies have obtained substantial compost microbiomes, yet the expressions and functions of these lignocellulolytic enzymes remains obscure. Thus, the discovery of thermophilic microorganisms as considerable biochemical catalysts for biofuels is becoming more and more attractive.Results A lignocellulose degrading strain isolated from thermophilic compost was identified as Geobacillus stearothermophilus B5, which could secrete considerable enzymes at the optimal temperature (60°C) and pH (7.5). One single contig of 3.37 Mbp was obtained from raw data and 3371 protein-coding genes were predicted, and the clusters of orthologous groups (COG) analysis revealed various genes with function of polymeric substrates degradation, especially for abundant CAZymes including glycoside hydrolases (GH, 29%) and glycosyl transferases (GT, 36%). Furthermore, the transcriptional responses of B5 at different temperature by using rice straw as sole carbon sources were also analyzed, based on which the mechanism of lignocellulose degradation at high temperature was revealed that B5 could resist the heat by up-regulating the heat shock proteins (HSP) and then secrete various Carbohydrate-Active enzymes (CAZymes) to realize energy balance.Conclusions The comparative whole-genome along with transcriptome analysis indicated that G. stearothermophilus B5 owned the ability of lignocellulose degradation and could be considered as a potential inoculant in composting efficiency, thus are also valuable for the lignocellulosic bioenergy industry.

scholarly journals Genome Sequence of Geobacillus stearothermophilus DSM 458, an Antimicrobial-Producing Thermophilic Bacterium, Isolated from a Sugar Beet Factory

2017 ◽  
Vol 5 (43) ◽  
Author(s):  
Kevin Egan ◽  
Philip Kelleher ◽  
Des Field ◽  
Mary C. Rea ◽  
R. Paul Ross ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Genome Sequence ◽  
In Silico ◽  
Thermophilic Bacterium ◽  
Full Genome Sequence ◽  
Full Genome ◽  
Geobacillus Stearothermophilus ◽  
Biosynthetic Genes ◽  
Content Type

ABSTRACT This paper reports the full genome sequence of the antimicrobial-producing bacterium Geobacillus stearothermophilus DSM 458, isolated in a sugar beet factory in Austria. In silico analysis reveals the presence of a number of novel bacteriocin biosynthetic genes.

scholarly journals Metagenomic Analysis of Stress Genes in Microbial Mat Communities from Antarctica and the High Arctic

2011 ◽  
Vol 78 (2) ◽  
pp. 549-559 ◽  
Author(s):  
Thibault Varin ◽  
Connie Lovejoy ◽  
Anne D. Jungblut ◽  
Warwick F. Vincent ◽  
Jacques Corbeil
Keyword(s):  
High Arctic ◽  
Environmental Stresses ◽  
The Arctic ◽  
Functional Responses ◽  
Protein Coding ◽  
Content Type ◽  
Stress Genes ◽  
Cyanobacterial Genes ◽  
Shock Proteins ◽  
The Antarctic

ABSTRACTPolar and alpine microbial communities experience a variety of environmental stresses, including perennial cold and freezing; however, knowledge of genomic responses to such conditions is still rudimentary. We analyzed the metagenomes of cyanobacterial mats from Arctic and Antarctic ice shelves, using high-throughput pyrosequencing to test the hypotheses that consortia from these extreme polar habitats were similar in terms of major phyla and subphyla and consequently in their potential responses to environmental stresses. Statistical comparisons of the protein-coding genes showed similarities between the mats from the two poles, with the majority of genes derived fromProteobacteriaandCyanobacteria; however, the relative proportions differed, with cyanobacterial genes more prevalent in the Antarctic mat metagenome. Other differences included a higher representation ofActinobacteriaandAlphaproteobacteriain the Arctic metagenomes, which may reflect the greater access to diasporas from both adjacent ice-free lands and the open ocean. Genes coding for functional responses to environmental stress (exopolysaccharides, cold shock proteins, and membrane modifications) were found in all of the metagenomes. However, in keeping with the greater exposure of the Arctic to long-range pollutants, sequences assigned to copper homeostasis genes were statistically (30%) more abundant in the Arctic samples. In contrast, more reads matching the sigma B genes were identified in the Antarctic mat, likely reflecting the more severe osmotic stress during freeze-up of the Antarctic ponds. This study underscores the presence of diverse mechanisms of adaptation to cold and other stresses in polar mats, consistent with the proportional representation of major bacterial groups.

scholarly journals Draft genome assembly data of Anoxybacillus sp. strain MB8 isolated from Tattapani hot springs, India

2021 ◽  
Author(s):  
VISHNU PRASOODANAN P K ◽  
Shruti S. Menon ◽  
Rituja Saxena ◽  
Prashant Waiker ◽  
Vineet K Sharma
Keyword(s):  
Hot Springs ◽  
De Novo ◽  
Draft Genome ◽  
Gc Content ◽  
Central India ◽  
Glycoside Hydrolases ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Protein Coding ◽  
Protein Coding Genes

Discovery of novel thermophiles has shown promising applications in the field of biotechnology. Due to their thermal stability, they can survive the harsh processes in the industries, which make them important to be characterized and studied. Members of Anoxybacillus are alkaline tolerant thermophiles and have been extensively isolated from manure, dairy-processed plants, and geothermal hot springs. This article reports the assembled data of an aerobic bacterium Anoxybacillus sp. strain MB8, isolated from the Tattapani hot springs in Central India, where the 16S rRNA gene shares an identity of 97% (99% coverage) with Anoxybacillus kamchatkensis strain G10. The de novo assembly and annotation performed on the genome of Anoxybacillus sp. strain MB8 comprises of 2,898,780 bp (in 190 contigs) with a GC content of 41.8% and includes 2,976 protein-coding genes,1 rRNA operon, 73 tRNAs, 1 tm-RNA and 10 CRISPR arrays. The predicted protein-coding genes have been classified into 21 eggNOG categories. The KEGG Automated Annotation Server (KAAS) analysis indicated the presence of assimilatory sulfate reduction pathway, nitrate reducing pathway, and genes for glycoside hydrolases (GHs) and glycoside transferase (GTs). GHs and GTs hold widespread applications, in the baking and food industry for bread manufacturing, and in the paper, detergent and cosmetic industry. Hence, Anoxybacillus sp. strain MB8 holds the potential to be screened and characterized for such commercially relevant enzymes.

scholarly journals Complete Genome Sequence of the Polysaccharide-Degrading Rumen Bacterium Pseudobutyrivibrio xylanivorans MA3014

2020 ◽  
Author(s):  
Nikola Palevich ◽  
Paul H. Maclean ◽  
William J. Kelly ◽  
Sinead C. Leahy ◽  
Jasna Rakonjac ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Bacterial Species ◽  
Glycoside Hydrolases ◽  
Rumen Bacterium ◽  
Protein Coding ◽  
Plant Polysaccharides ◽  
Plant Matter ◽  
Genes Encoding

AbstractRuminants are essential for maintaining the global population and managing greenhouse gas emissions. In the rumen, bacterial species belonging to the genera rumen Butyrivibrio and Pseudobutyrivibrio constitute the core bacterial rumen microbiome and are important degraders of plant-derived complex polysaccharides. Pseudobutyrivibrio xylanivorans MA3014 was selected for genome sequencing in order to examine its ability to breakdown and utilize plant polysaccharides. The complete genome sequence of MA3014 is 3.58 Mb, consists of three replicons (a chromosome, chromid and plasmid), has an overall G+C content of 39.6% and encodes 3,265 putative protein-coding genes (PCGs). Comparative pan-genomics of all cultivated and currently available P. xylanivorans genomes has revealed highly open genomes and a strong correlation of orthologous genes within this species of rumen bacteria. MA3014 is metabolically versatile and capable of utilizing a range of simple mono-or oligosaccharides to complex plant polysaccharides such as pectins, mannans, starch and hemicelluloses for growth, with lactate, butyrate and formate as the principal fermentation end-products. The genes encoding these metabolic pathways have been identified and MA3014 is predicted to encode an extensive repertoire of Carbohydrate-Active enZYmes (CAZymes) with 80 Glycoside Hydrolases (GHs), 28 Carbohydrate Esterases (CEs) and 51 Glycosyl Transferases (GTs), that suggest its role as an initiator of primary solubilization of plant matter in the rumen.

scholarly journals Identification of an Oligosaccharide Dehydrogenase from Pycnoporus Cinnabarinus Provides Insights into Fungal Breakdown of Lignocellulose

2021 ◽  
Author(s):  
Gabriele Cerutti ◽  
Elena Gugole ◽  
Linda Celeste Montemiglio ◽  
Annick Turbé-Doan ◽  
Dehbia Chena ◽  
...  
Keyword(s):  
Function Analysis ◽  
Sequence Similarity ◽  
Functional Characterization ◽  
Physiological Role ◽  
Free Form ◽  
Lignocellulose Degradation ◽  
Carbohydrate Active Enzymes ◽  
Recognition Mechanism ◽  
Pycnoporus Cinnabarinus ◽  
Enzymatic Function

Abstract Background: Fungal glucose dehydrogenases (GDHs) are FAD-dependent enzymes belonging to the glucose-methanol-choline oxidoreductase superfamily. These enzymes are classified in the “Auxiliary Activity” family 3 (AA3) of the Carbohydrate-Active enZymes database, and more specifically in subfamily AA3_2, that also includes the closely related flavoenzymes aryl-alcohol oxidase and glucose 1-oxidase. Based on sequence similarity to known fungal GDHs, an AA3_2 enzyme active on glucose was identified in the genome of Pycnoporus cinnabarinus, a model Basidiomycete able to completely degrade lignin.Results: In our work, substrate screening and functional characterization showed an unexpected preferential activity of this enzyme toward oligosaccharides containing a b(1à3) glycosidic bond, with the highest efficiency observed for the disaccharide laminaribiose. Despite its sequence similarity to GDHs, we defined a novel enzymatic activity, namely oligosaccharide dehydrogenase (ODH), for this enzyme. The crystallographic structures of ODH in the sugar-free form and in complex with glucose and laminaribiose unveiled a peculiar saccharide recognition mechanism which is not shared with previously characterized AA3 oxidoreductases and accounts for ODH preferential activity toward oligosaccharides. The sugar molecules in the active site of ODH are mainly stabilized through CH-p interactions with aromatic residues rather than through hydrogen bonds with highly conserved residues, as observed instead for the fungal glucose dehydrogenases and oxidases characterized to date. Finally, three sugar-binding sites were identified on ODH external surface, which were not previously observed and might be of importance in the physiological scenario.Conclusions: Structure-function analysis of ODH is consistent with its role as an auxiliary enzyme in lignocellulose degradation and unveils yet another enzymatic function within the AA3 family of the Carbohydrate-Active enZymes database. Our findings allow deciphering the molecular determinants of substrate binding and provide insight into the physiological role of ODH, opening new perspectives to exploit biodiversity for lignocellulose transformation into fuels and chemicals.

scholarly journals Evolutionary diversification of tiny ocean predators

2020 ◽  
Author(s):  
Francisco Latorre ◽  
Ina M. Deutschmann ◽  
Aurelie Labarre ◽  
Aleix Obiol ◽  
Anders Krabberød ◽  
...  
Keyword(s):  
Single Cells ◽  
Prey Type ◽  
Distribution Patterns ◽  
Trophic Levels ◽  
Glycoside Hydrolases ◽  
Global Ocean ◽  
Heterotrophic Flagellates ◽  
Evolutionary Diversification ◽  
Niche Adaptation ◽  
Different Temperatures

ABSTRACTUnicellular eukaryotic predators have a crucial role in the functioning of the ocean ecosystem by recycling nutrients and energy that are channeled to upper trophic levels. Traditionally, these evolutionary-diverse organisms have been combined into a single functional group (Heterotrophic flagellates), overlooking their organismal differences. Here we investigate four evolutionary related species belonging to one cosmopolitan family of uncultured marine picoeukaryotic predators: MAST-4 (species A, B, C, and E). Co-occurrence and distribution analyses in the global surface ocean indicated contrasting patterns in MAST-4A & C, suggesting adaptation to different temperatures. We then investigated whether these spatial distribution patterns were mirrored by MAST-4 genomic content using Single-Cell Genomics. Analyses of 69 single-cells recovered 66-83% of the MAST-4A/B/C/E genomes, which displayed substantial inter-species divergence. MAST-4 genomes were similar in terms of broad gene functional categories, but they differed in enzymes of ecological relevance, such as glycoside hydrolases (GHs), which are part of the food degradation machinery in MAST-4. Interestingly, MAST-4 species featuring a similar GH composition co-excluded each other (A & C) in the surface global ocean, while species with a different set of GHs appeared to be able to co-exist (species B & C) suggesting further niche diversification associated to prey digestion. We propose that differential niche adaptation to temperature and prey type has promoted adaptive evolutionary diversification in MAST-4. Altogether, we show that minute ocean predators from the same family may have different biogeography and genomic content, which need to be accounted to better comprehend marine food webs.

scholarly journals Identification of a New Heavy-Metal-Resistant Strain of Geobacillus stearothermophilus Isolated from a Hydrothermally Active Volcanic Area in Southern Italy

2020 ◽  
Vol 17 (8) ◽  
pp. 2678
Author(s):  
Rosanna Puopolo ◽  
Giovanni Gallo ◽  
Angela Mormone ◽  
Danila Limauro ◽  
Patrizia Contursi ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Hot Springs ◽  
Toxic Metal ◽  
Metal Resistance ◽  
Thermophilic Bacterium ◽  
Campi Flegrei ◽  
Volcanic Area ◽  
The Novel ◽  
Geobacillus Stearothermophilus ◽  
Rrna Sequencing

Microorganisms thriving in hot springs and hydrothermally active volcanic areas are dynamically involved in heavy-metal biogeochemical cycles; they have developed peculiar resistance systems to cope with such metals which nowadays can be considered among the most permanent and toxic pollutants for humans and the environment. For this reason, their exploitation is functional to unravel mechanisms of toxic-metal detoxification and to address bioremediation of heavy-metal pollution with eco-sustainable approaches. In this work, we isolated a novel strain of the thermophilic bacterium Geobacillus stearothermophilus from the solfataric mud pool in Pisciarelli, a well-known hydrothermally active zone of the Campi Flegrei volcano located near Naples in Italy, and characterized it by ribotyping, 16S rRNA sequencing and mass spectrometry analyses. The minimal inhibitory concentration (MIC) toward several heavy-metal ions indicated that the novel G. stearothermophilus isolate is particularly resistant to some of them. Functional and morphological analyses suggest that it is endowed with metal resistance systems for arsenic and cadmium detoxification.

scholarly journals Draft Genome Sequence of the Thermophilic Acetogen Moorella humiferrea DSM 23265

2018 ◽  
Vol 6 (17) ◽  
Author(s):  
Anja Poehlein ◽  
Alisa Keyl ◽  
Jan C. Milsch ◽  
Rolf Daniel
Keyword(s):  
Humic Acid ◽  
Genome Sequence ◽  
Draft Genome ◽  
Thermophilic Bacterium ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Content Type ◽  
Electron Shuttling ◽  
Protein Coding Genes ◽  
Hydrothermal Spring

ABSTRACT Moorella humiferrea is an endospore-forming, anaerobic, and thermophilic bacterium which was isolated from a terrestrial hydrothermal spring. M. humiferrea is able to use humic acid or 10-anthraquinone-2,6-disulfonate as an electron-shuttling compound for growth and Fe(III) reduction. The genome has a size of 2.629 Mb and contains 2,668 predicted protein-coding genes.

The glycoconjugate-degrading enzymes of Clostridium perfringens: Tailored catalysts for breaching the intestinal mucus barrier

Glycobiology ◽  
2020 ◽  
Author(s):  
Kristin E Low ◽  
Steven P Smith ◽  
D Wade Abbott ◽  
Alisdair B Boraston
Keyword(s):  
Clostridium Perfringens ◽  
Bacterial Species ◽  
Opportunistic Pathogen ◽  
Glycoside Hydrolases ◽  
Necrotic Enteritis ◽  
Carbohydrate Active Enzymes ◽  
Intestinal Mucus ◽  
Mucosal Layer ◽  
Potential Component ◽  
Mucus Barrier

Abstract The gastrointestinal (GI) tract of humans and animals is lined with mucus that serves as a barrier between the gut microbiota and the epithelial layer of the intestine. As the proteins present in mucus are typically heavily glycosylated, such as the mucins, several enteric commensal and pathogenic bacterial species are well-adapted to this rich carbon source and their genomes are replete with carbohydrate-active enzymes targeted toward dismantling the glycans and proteins present in mucus. One such species is Clostridium perfringens, a Gram-positive opportunistic pathogen indigenous to the gut of humans and animals. The genome of C. perfringens encodes numerous carbohydrate-active enzymes that are predicted or known to target glycosidic linkages within or on the termini of mucus glycans. Through this enzymatic activity, the degradation of the mucosal layer by C. perfringens has been implicated in a number of GI diseases, the most severe of which is necrotic enteritis. In this review, we describe the wide array of extracellular glycoside hydrolases, and their accessory modules, that is possessed by C. perfringens, and examine the unique multimodularity of these proteins in the context of degrading the glycoconjugates in mucus as a potential component of disease.

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