scholarly journals Sequence based prediction of novel domains in the cellulosome ofRuminiclostridium thermocellum

2016 ◽  
Author(s):  
Zarrin Basharat ◽  
Azra Yasmin
Keyword(s):  
Protein Domain ◽  
Biofuel Production ◽  
Biological Information ◽  
Crystalline Cellulose ◽  
New Information ◽  
Refseq Protein ◽  
Genes Encoding ◽  
Rapid Generation ◽  
Domain Discovery ◽  
Generation Biofuel

AbstractRuminiclostridium thermocellumstrain ATCC 27405 is valuable with reference to the next generation biofuel production being a degrader of crystalline cellulose. The completion of its genome sequence has revealed that this organism carries 3,376 genes with more than hundred genes encoding for enzymes involved in cellulysis. Novel protein domain discovery in the cellulose degrading enzyme complex of this strain has been attempted to understand this organism at molecular level. Streamlined automated methods were employed to generate possibly unreported or new domains. A set of 12 novel Pfam-B domains was developed after detailed analysis. This finding will enhance our understanding of this bacterium and its molecular processes involved in the degradation of cellulose. This approach ofin silicoanalysis prior to experimentation facilitates in lab study. Previously uncorrelated data has been utilized for rapid generation of new biological information in this study.NoteThis research was conducted in 2014 forClostridium thermocellumATCC 27405. The bacterium was later reannotated asRuminiclostridium thermocellum. See NCBI nonredundant RefSeq protein annotation details athttp://www.ncbi.nlm.nih.gov/refseq/about/prokaryotes/reannotation/. The study utilizes Pfam-B database, which was discontinued with effect from release 28.0 (5/2015). Availability of new information, reannotation/modification in accession numbers might impact some of the analyzed values although effort has been made to provide latest accession numbers and reference strain parameters. The preprint version may contain grammatical and proofreading mistakes. Errors and omissions excepted.

scholarly journals Re-annotation of the genome sequence of Helicobacter pylori 26695

2013 ◽  
Vol 10 (3) ◽  
pp. 66-78 ◽  
Author(s):  
Tiago Resende ◽  
Daniela M. Correia ◽  
Miguel Rocha ◽  
Isabel Rocha
Keyword(s):  
Helicobacter Pylori ◽  
Metabolic Model ◽  
Relevant Information ◽  
Biological Information ◽  
Gastric Ulcers ◽  
Metabolic Genes ◽  
New Information ◽  
Genes Encoding ◽  
On Line ◽  
H Pylori

Summary Helicobacter pylori is a pathogenic bacterium that colonizes the human epithelia, causing duodenal and gastric ulcers, and gastric cancer. The genome of H. pylori 26695 has been previously sequenced and annotated. In addition, two genome-scale metabolic models have been developed. In order to maintain accurate and relevant information on coding sequences (CDS) and to retrieve new information, the assignment of new functions to Helicobacter pylori 26695s genes was performed in this work. The use of software tools, on-line databases and an annotation pipeline for inspecting each gene allowed the attribution of validated EC numbers and TC numbers to metabolic genes encoding enzymes and transport proteins, respectively. 1212 genes encoding proteins were identified in this annotation, being 712 metabolic genes and 500 non-metabolic, while 191 new functions were assignment to the CDS of this bacterium. This information provides relevant biological information for the scientific community dealing with this organism and can be used as the basis for a new metabolic model reconstruction.

scholarly journals Effect of temperature and surfactant on biomass growth and higher-alcohol production during syngas fermentation by Clostridium carboxidivorans P7

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Shaohuang Shen ◽  
Guan Wang ◽  
Ming Zhang ◽  
Yin Tang ◽  
Yang Gu ◽  
...  
Keyword(s):  
Tween 80 ◽  
Biofuel Production ◽  
Effect Of Temperature ◽  
Biomass Growth ◽  
Syngas Fermentation ◽  
Higher Alcohol ◽  
Alcohol Production ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Clostridium Carboxidivorans

Abstract Hexanol–butanol–ethanol fermentation from syngas by Clostridium carboxidivorans P7 is a promising route for biofuel production. However, bacterial agglomeration in the culture of 37 °C severely hampers the accumulation of biomass and products. To investigate the effect of culture temperature on biomass growth and higher-alcohol production, C. carboxidivorans P7 was cultivated at both constant and two-step temperatures in the range from 25 to 37 °C. Meanwhile, Tween-80 and saponin were screened out from eight surfactants to alleviate agglomeration at 37 °C. The results showed that enhanced higher-alcohol production was contributed mainly by the application of two-step temperature culture rather than the addition of anti-agglomeration surfactants. Furthermore, comparative transcriptome revealed that although 37 °C promoted high expression of genes involved in the Wood–Ljungdahl pathway, genes encoding enzymes catalyzing acyl-condensation reactions associated with higher-alcohol production were highly expressed at 25 °C. This study gained greater insight into temperature-effect mechanism on syngas fermentation by C. carboxidivorans P7.

scholarly journals Techno-economic analysis for co-processing fast pyrolysis liquid with vacuum gasoil in FCC units for second-generation biofuel production

Fuel ◽  
2021 ◽  
Vol 293 ◽  
pp. 119960
Author(s):  
Michael Talmadge ◽  
Christopher Kinchin ◽  
Helena Li Chum ◽  
Andrea de Rezende Pinho ◽  
Mary Biddy ◽  
...  
Keyword(s):  
Economic Analysis ◽  
Second Generation ◽  
Fast Pyrolysis ◽  
Vacuum Gasoil ◽  
Biofuel Production ◽  
Pyrolysis Liquid ◽  
Generation Biofuel ◽  
Fast Pyrolysis Liquid

scholarly journals A Non-negative Matrix Factorization Based Method for Identifying Essential Proteins

2021 ◽  
Author(s):  
Zhihong Zhang ◽  
Sai Hu ◽  
Wei Yan ◽  
Bihai Zhao ◽  
Lei Wang
Keyword(s):  
Protein Interaction ◽  
Matrix Factorization ◽  
Biological Data ◽  
Protein Domain ◽  
Biological Information ◽  
Ppi Network ◽  
Essential Proteins ◽  
Protein Protein Interaction ◽  
Ppi Networks ◽  
Non Negative Matrix Factorization

Abstract BackgroundIdentification of essential proteins is very important for understanding the basic requirements to sustain a living organism. In recent years, various different computational methods have been proposed to identify essential proteins based on protein-protein interaction (PPI) networks. However, there has been reliable evidence that a huge amount of false negatives and false positives exist in PPI data. Therefore, it is necessary to reduce the influence of false data on accuracy of essential proteins prediction by integrating multi-source biological information with PPI networks.ResultsIn this paper, we proposed a non-negative matrix factorization and multiple biological information based model (NDM) for identifying essential proteins. The first stage in this progress was to construct a weighted PPI network by combing the information of protein domain, protein complex and the topology characteristic of the original PPI network. Then, the non-negative matrix factorization technique was used to reconstruct an optimized PPI network with whole enough weight of edges. In the final stage, the ranking score of each protein was computed by the PageRank algorithm in which the initial scores were calculated with homologous and subcellular localization information. In order to verify the effectiveness of the NDM method, we compared the NDM with other state-of-the-art essential proteins prediction methods. The comparison of the results obtained from different methods indicated that our NDM model has better performance in predicting essential proteins.ConclusionEmploying the non-negative matrix factorization and integrating multi-source biological data can effectively improve quality of the PPI network, which resulted in the led to optimization of the performance essential proteins identification. This will also provide a new perspective for other prediction based on protein-protein interaction networks.

scholarly journals Genome Sequence of the Cellulolytic Gliding Bacterium Cytophaga hutchinsonii

2007 ◽  
Vol 73 (11) ◽  
pp. 3536-3546 ◽  
Author(s):  
Gary Xie ◽  
David C. Bruce ◽  
Jean F. Challacombe ◽  
Olga Chertkov ◽  
John C. Detter ◽  
...  
Keyword(s):  
Gliding Motility ◽  
Open Reading Frames ◽  
Crystalline Cellulose ◽  
Cellulolytic Bacteria ◽  
Cytophaga Hutchinsonii ◽  
Type Iv ◽  
Flavobacterium Johnsoniae ◽  
Anchoring Proteins ◽  
Genes Encoding ◽  
Gliding Bacterium

ABSTRACT The complete DNA sequence of the aerobic cellulolytic soil bacterium Cytophaga hutchinsonii, which belongs to the phylum Bacteroidetes, is presented. The genome consists of a single, circular, 4.43-Mb chromosome containing 3,790 open reading frames, 1,986 of which have been assigned a tentative function. Two of the most striking characteristics of C. hutchinsonii are its rapid gliding motility over surfaces and its contact-dependent digestion of crystalline cellulose. The mechanism of C. hutchinsonii motility is not known, but its genome contains homologs for each of the gld genes that are required for gliding of the distantly related bacteroidete Flavobacterium johnsoniae. Cytophaga-Flavobacterium gliding appears to be novel and does not involve well-studied motility organelles such as flagella or type IV pili. Many genes thought to encode proteins involved in cellulose utilization were identified. These include candidate endo-β-1,4-glucanases and β-glucosidases. Surprisingly, obvious homologs of known cellobiohydrolases were not detected. Since such enzymes are needed for efficient cellulose digestion by well-studied cellulolytic bacteria, C. hutchinsonii either has novel cellobiohydrolases or has an unusual method of cellulose utilization. Genes encoding proteins with cohesin domains, which are characteristic of cellulosomes, were absent, but many proteins predicted to be involved in polysaccharide utilization had putative D5 domains, which are thought to be involved in anchoring proteins to the cell surface.

scholarly journals Enzyme Diversity of the Cellulolytic System Produced by Clostridium cellulolyticum Explored by Two-Dimensional Analysis: Identification of Seven Genes Encoding New Dockerin-Containing Proteins

2007 ◽  
Vol 189 (6) ◽  
pp. 2300-2309 ◽  
Author(s):  
Jean-Charles Blouzard ◽  
Caroline Bourgeois ◽  
Pascale de Philip ◽  
Odile Valette ◽  
Anne Bélaïch ◽  
...  
Keyword(s):  
Energy Source ◽  
Glycoside Hydrolase ◽  
Glycoside Hydrolases ◽  
Crystalline Cellulose ◽  
Two Dimensional ◽  
Specific Antibodies ◽  
Two Dimensional Electrophoresis ◽  
Clostridium Cellulolyticum ◽  
Genes Encoding ◽  
Dimensional Electrophoresis

ABSTRACT The enzyme diversity of the cellulolytic system produced by Clostridium cellulolyticum grown on crystalline cellulose as a sole carbon and energy source was explored by two-dimensional electrophoresis. The cellulolytic system of C. cellulolyticum is composed of at least 30 dockerin-containing proteins (designated cellulosomal proteins) and 30 noncellulosomal components. Most of the known cellulosomal proteins, including CipC, Cel48F, Cel8C, Cel9G, Cel9E, Man5K, Cel9M, and Cel5A, were identified by using two-dimensional Western blot analysis with specific antibodies, whereas Cel5N, Cel9J, and Cel44O were identified by using N-terminal sequencing. Unknown enzymes having carboxymethyl cellulase or xylanase activities were detected by zymogram analysis of two-dimensional gels. Some of these enzymes were identified by N-terminal sequencing as homologs of proteins listed in the NCBI database. Using Trap-Dock PCR and DNA walking, seven genes encoding new dockerin-containing proteins were cloned and sequenced. Some of these genes are clustered. Enzymes encoded by these genes belong to glycoside hydrolase families GH2, GH9, GH10, GH26, GH27, and GH59. Except for members of family GH9, which contains only cellulases, the new modular glycoside hydrolases discovered in this work could be involved in the degradation of different hemicellulosic substrates, such as xylan or galactomannan.

scholarly journals Gene Integration and Expression and Extracellular Secretion of Erwinia chrysanthemi Endoglucanase CelY (celY) and CelZ (celZ) in EthanologenicKlebsiella oxytoca P2

2001 ◽  
Vol 67 (1) ◽  
pp. 6-14 ◽  
Author(s):  
Shengde Zhou ◽  
F. C. Davis ◽  
L. O. Ingram
Keyword(s):  
Fermentation Broth ◽  
Klebsiella Oxytoca ◽  
Cellulase Activity ◽  
Erwinia Chrysanthemi ◽  
Crystalline Cellulose ◽  
Fungal Enzymes ◽  
Extracellular Milieu ◽  
Extracellular Secretion ◽  
Genes Encoding ◽  
Fuels And Chemicals

ABSTRACT The development of methods to reduce costs associated with the solubilization of cellulose is essential for the utilization of lignocellulose as a renewable feedstock for fuels and chemicals. One promising approach is the genetic engineering of ethanol-producing microorganisms that also produce cellulase enzymes during fermentation. By starting with an ethanologenic derivative (strain P2) ofKlebsiella oxytoca M5A1 with the native ability to metabolize cellobiose, the need for supplemental β-glucosidase was previously eliminated. In the current study, this approach has been extended by adding genes encoding endoglucanase activities. GenescelY and celZ from Erwinia chrysanthemi have been functionally integrated into the chromosome of P2 using surrogate promoters from Zymomonas mobilis for expression. Both were secreted into the extracellular milieu, producing more than 20,000 endoglucanase units (carboxymethyl cellulase activity) per liter of fermentation broth. During the fermentation of crystalline cellulose with low levels of commercial cellulases of fungal origin, these new strains produced up to 22% more ethanol than unmodified P2. Most of the beneficial contribution was attributed to CelY rather than to CelZ. These results suggest that fungal enzymes with substrate profiles resembling CelY (preference for long-chain polymers and lack of activity on soluble cello-oligosaccharides of two to five glucosyl residues) may be limiting in commercial cellulase preparations.

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