• Journal of Microbiology and Biotechnology
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• v.27 no.3
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• pp.514-523
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• 2017

Carbon catabolite repression is a crucial regulation mechanism in microorganisms, but its characteristic in Rhizopus is still unclear. We extracted a carbon regulation gene, cre, that encoded a carbon catabolite repressor protein (CRE) from Rhizopus stolonifer TP-02, and studied the regulation of CRE by real-time qPCR. CRE responded to glucose in a certain range, where it could significantly regulate part of the cellulase genes (eg, bg, and cbh2) without cbh1. In the comparison of the response of cre and four cellulase genes to carboxymethylcellulose sodium and a simple carbon source (lactose), the effect of CRE was only related to the concentration of reducing sugars. By regulating the reducing sugars to range from 0.4% to 0.6%, a glucose-containing medium with lactose as the inducer could effectively induce cellulases without the repression of CRE. This regulation method could potentially reduce the cost of enzymes produced in industries and provide a possible solution to achieve the largescale synthesis of cellulases.

• Journal of Microbiology and Biotechnology
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• v.28 no.9
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• pp.1473-1481
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• 2018

A cellulase hyperproducing mutant strain, JNDY-13, was obtained using the ARTP mutation system and with Trichoderma reesei RUT-C30 as the parent strain. Whole-genome sequencing of JNDY-13 confirmed that 105 of the 653 SNPs were point mutations, 336 mutations were deletions and 165 were insertions. Moreover, 99 mutations were insertions and duplications. Among all the mutations, the one that occurred in the galactokinase gene might be related to the production of cellulases in T. reesei JNDY-13. Moreover, the up-regulation of cellulase and hemicellulase genes in JNDY-13 might contribute to higher cellulases production. Under optimal conditions, the highest cellulase activity by batch fermentation reached 4.35 U/ml, and the highest activity of fed-batch fermentation achieved was 5.40 U/ml.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.8
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• pp.1144-1151
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• 2013

In this study, protein domains with cellulase activity in goat rumen microbes were investigated using metagenomic and bioinformatic analyses. After the complete genome of goat rumen microbes was obtained using a shotgun sequencing method, 217,892,109 pair reads were filtered, including only those with 70% identity, 100-bp matches, and thresholds below $E^{-10}$ using METAIDBA. These filtered contigs were assembled and annotated using blastN against the NCBI nucleotide database. As a result, a microbial community structure with 1431 species was analyzed, among which Prevotella ruminicola 23 bacteria and Butyrivibrio proteoclasticus B316 were the dominant groups. In parallel, 201 sequences related with cellulase activities (EC.3.2.1.4) were obtained through blast searches using the enzyme.dat file provided by the NCBI database. After translating the nucleotide sequence into a protein sequence using Interproscan, 28 protein domains with cellulase activity were identified using the HMMER package with threshold E values below $10^{-5}$. Cellulase activity protein domain profiling showed that the major protein domains such as lipase GDSL, cellulase, and Glyco hydro 10 were present in bacterial species with strong cellulase activities. Furthermore, correlation plots clearly displayed the strong positive correlation between some protein domain groups, which was indicative of microbial adaption in the goat rumen based on feeding habits. This is the first metagenomic analysis of cellulase activity protein domains using bioinformatics from the goat rumen.

• Journal of Life Science
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• v.25 no.6
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• pp.680-685
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• 2015

Previously, cellulase and xylanase producing microorganism, Bacillus subtilis NC1, was isolated from soil. Based on the 16S rRNA gene sequence and API 50 CHL test the strain was identified as Bacillus subtilis, and named as B. subtilis NC1. We cloned and sequenced the genes for cellulase and xylanase. Plus, the deduced amino acid sequences from the genes of cellulase and xylanase were determined and were also identified as glycosyl hydrolases family (GH) 5 and 30, respectively. In this study to optimize the medium parameters for cellulase production by B. subtilis NC1 the RSM (response surface methodology) based on CCD (central composite design) model was performed. Three factors, tryptone, yeast extract, and NaCl, for N or C source were investigated. The cellulase activity was measured with a carboxylmethyl cellulose (CMC) plate and the 3,5-dinitrosalicylic acid (DNS) methods. The coefficient of determination (R²) for the model was 0.960, and the probability value (p=0.0001) of the regression model was highly significant. Based on the RSM, the optimum conditions for cellulase production by B. subtilis NC1 were predicted to be tryptone of 2.5%, yeast extract of 0.5%, and NaCl of 1.0%. Through the model verification, cellulase activity of Bacillus subtilis NC1 increased from 0.5 to 0.62 U/ml (24%) compared to the original medium.

• The Plant Pathology Journal
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• v.24 no.2
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• pp.143-151
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• 2008

To define the functions of the rpf genes in Xanthomonas oryzae pv. oryzae (Xoo), which regulates pathogenicity factors in Xanthomonas campestris pv. campestris (Xcc), marker-exchange mutants of each rpf gene were generated. When the mutants were inoculated on a susceptible cultivar, the lesion lengths caused by the rpfB, rpfC, rpfF, and rpfG mutants were significantly smaller than those caused by the wild type, whereas those caused by the rpfA, rpfD, and rpfI mutants were not. Several virulence determinants, including extracellular polysaccharide (EPS) production, xylanase production, and motility, were significantly decreased in the four mutants. However, the cellulase activity in the mutants was unchanged. Complementation of the rpfB and rpfC mutations restored the virulence and the expression of the virulence determinants. Expression analysis of 14 virulence genes revealed that the expression of genes related to EPS production (gumG and gumM), LPS (xanA, xanB, wxoD, and wxoC), phytase (phyA), xylanase (xynB), lipase (lipA), and motility (pitA) were reduced significantly in the mutants rpfB, rpfC, rpfF, and rpfG. In contrast, the expression of genes related to cellulase (eglxob, clsA), cellobiosidase (cbsA), and iron metabolism (fur) was unchanged. The results of this study clearly show that rpfB, rpfC, rpfF, and rpfG are important for the virulence of Xoo KACC10859, and that virulence genes are regulated differently by the Rpfs.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.6
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• pp.880-884
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• 2001

Rumen microbiology research has undergone several evolutionary steps: the isolation and nutritional characterization of readily cultivated microbes; followed by the cloning and sequence analysis of individual genes relevant to key digestive processes; through to the use of small subunit ribosomal RNA (SSU rRNA) sequences for a cultivation-independent examination of microbial diversity. Our knowledge of rumen microbiology has expanded as a result, but the translation of this information into productive alterations of ruminal function has been rather limited. For instance, the cloning and characterization of cellulase genes in Escherichia coli has yielded some valuable information about this complex enzyme system in ruminal bacteria. SSU rRNA analyses have also confirmed that a considerable amount of the microbial diversity in the rumen is not represented in existing culture collections. However, we still have little idea of whether the key, and potentially rate-limiting, gene products and (or) microbial interactions have been identified. Technologies allowing high throughput nucleotide and protein sequence analysis have led to the emergence of two new fields of investigation, genomics and proteomics. Both disciplines can be further subdivided into functional and comparative lines of investigation. The massive accumulation of microbial DNA and protein sequence data, including complete genome sequences, is revolutionizing the way we examine microbial physiology and diversity. We describe here some examples of our use of genomics- and proteomics-based methods, to analyze the cellulase system of Ruminococcus flavefaciens FD-1 and explore the genome of Ruminococcus albus 8. At Illinois, we are using bacterial artificial chromosome (BAC) vectors to create libraries containing large (>75 kbases), contiguous segments of DNA from R. flavefaciens FD-1. Considering that every bacterium is not a candidate for whole genome sequencing, BAC libraries offer an attractive, alternative method to perform physical and functional analyses of a bacterium's genome. Our first plan is to use these BAC clones to determine whether or not cellulases and accessory genes in R. flavefaciens exist in clusters of orthologous genes (COGs). Proteomics is also being used to complement the BAC library/DNA sequencing approach. Proteins differentially expressed in response to carbon source are being identified by 2-D SDS-PAGE, followed by in-gel-digests and peptide mass mapping by MALDI-TOF Mass Spectrometry, as well as peptide sequencing by Edman degradation. At Ohio State, we have used a combination of functional proteomics, mutational analysis and differential display RT-PCR to obtain evidence suggesting that in addition to a cellulosome-like mechanism, R. albus 8 possesses other mechanisms for adhesion to plant surfaces. Genome walking on either side of these differentially expressed transcripts has also resulted in two interesting observations: i) a relatively large number of genes with no matches in the current databases and; ii) the identification of genes with a high level of sequence identity to those identified, until now, in the archaebacteria. Genomics and proteomics will also accelerate our understanding of microbial interactions, and allow a greater degree of in situ analyses in the future. The challenge is to utilize genomics and proteomics to improve our fundamental understanding of microbial physiology, diversity and ecology, and overcome constraints to ruminal function.

• Journal of the Korean Wood Science and Technology
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• v.35 no.6
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• pp.166-174
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• 2007

To know the effect of enzymatic pre-treatment on softwood Kraft pulp, two xylanse-encoding genes, named xynl and xynll were isolated from Thrichoderma ressei. Structural genes of xylanase (XYNI, XYNII) and cellulase (EGIV-CBDII) were isolated from T. ressei and Rumicoccus albus respectively, and expressed in E. coli. bacterial culture. The specific activity of purified recombinant XYNI is higher than XYNII. The brightness of XYNI treated softwood Kraft pulp increased to 29.9%. On further sequential treatment with EGIV-CBDII and XYNI the brightness of softwood Kraft pulp were improved to 9.1 and 73% respectively. As expected the Kappa number of softwood Kraft pulp also decreased 8.1, 4.6 and 3.2% respectively. Results further indicate that this sequential combination of enzyme treatment has synergic effect for improving bleaching of softwood Kraft pulp.

• Biotechnology and Bioprocess Engineering:BBE
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• v.10 no.6
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• pp.482-493
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• 2005

Biomass is originally photosynthesized from inorgainic compounds such as $CO_2$, minerals, water and solar energy. Recent studies have shown that anaerobic bacteria have the ability to convert recalcitrant biomass such as cellullosic or chitinoic materials to useful compounds. The biomass containing agricultural waste, unutilized wood and other garbage is expected to utilize as feed, food and fuel by microbial degradation and other metabolic functions. In this study we isolated several anaerobic, cellulolytic and chitinolytic bacteria from rumen fluid, compost and soil to study their related enzymes and genes. The anaerobic and cellulolytic bacteria, Clostridium thermocellum, Clostridium stercorarium, and Clostridium josui, were isolated from compost and the chitinolytic Clostridium paraputrificum from beach soil and Ruminococcus albus was isolated from cow rumen. After isolation, novel cellulase and xylanase genes from these anaerobes were cloned and expressed in Escherichia coli. The properties of the cloned enzymes showed that some of them were the components of the enzyme (cellulase) complex, i.e., cellulosome, which is known to form complexes by binding cohesin domains on the cellulase integrating protein (Cip: or core protein) and dockerin domains on the enzymes. Several dockerin and cohesin polypeptides were independently produced by E. coli and their binding properties were specified with BIAcore by measuring surface plasmon resonance. Three pairs of cohesin-dockerin with differing binding specificities were selected. Two of their genes encoding their respective cohesin polypeptides were combined to one gene and expressed in E. coli as a chimeric core protein, on which two dockerin-dehydrogenase chimeras, the dockerin-formaldehyde dehydrogenase and the dockerin-NADH dehydrogenase are planning to bind for catalyzing $CO_2$ reduction to formic acid by feeding NADH. This reaction may represent a novel strategy for the reduction of the green house gases. Enzymes from the anaerobes were also expressed in tobacco and rice plants. The activity of a xylanase from C. stercorarium was detected in leaves, stems, and rice grain under the control of CaMV35S promoter. The digestibility of transgenic rice leaves in goat rumen was slightly accelerated. C. paraputrificum was found to solubilize shrimp shells and chitin to generate hydrogen gas. Hydrogen productivity (1.7 mol $H_2/mol$ glucos) of the organism was improved up to 1.8 times by additional expression of the own hydrogenase gene in C. paraputrficum using a modified vector of Clostridiu, perfringens. The hydrygen producing microflora from soil, garbage and dried pelletted garbage, known as refuse derived fuel(RDF), were also found to be effective in converting biomass waste to hydrogen gas.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.11
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• pp.1555-1565
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• 2009

Anaerobic rumen fungi have been regarded as good genetic resources for enzyme production which might be useful for feed supplements, bio-energy production, bio-remediation and other industrial purposes. In this study, an expressed sequence tag (EST) library of the rumen anaerobic fungus Neocallimastix frontalis was constructed and functional genes from the EST library were analyzed to elucidate carbohydrate metabolism of anaerobic fungi. From 10,080 acquired clones, 9,569 clones with average size of 628 bp were selected for analysis. After the assembling process, 1,410 contigs were assembled and 1,369 sequences remained as singletons. 1,192 sequences were matched with proteins in the public data base with known function and 693 of them were matched with proteins isolated from fungi. One hundred and fifty four sequences were classified as genes related with biological process and 328 sequences were classified as genes related with cellular components. Most of the enzymes in the pathway of glucose metabolism were successfully isolated via construction of 10,080 ESTs. Four kinds of hemi-cellulase were isolated such as mannanase, xylose isomerase, xylan esterase, and xylanase. Five $\beta$-glucosidases with at least three different conserved domain structures were isolated. Ten cellulases with at least five different conserved domain structures were isolated. This is the first solid data supporting the expression of a multiple enzyme system in the fungus N. frontalis for polysaccharide hydrolysis.

• Journal of Microbiology and Biotechnology
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• v.2 no.1
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• pp.50-55
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• 1992

A genomic library of a mesophilic cellulolytic anaerobe, Clostridium sp. KCTC 8440 DNA was constructed in Escherichia coli using plasmid pUC9. Clones of E. coli exhibiting carboxymethyl cellulose-hydrolyzing activity (CMCase) were isolated and divided into seven types based on the restriction enzyme patterns of recombinant plasmids. E. coli strains carrying type A genes showed activity on carboxymethyl cellulose about 7-8 times greater than clones carrying genes of other types. Restriction maps of the cloned DNA fragments were determined, and homologies between them were investigated. The results suggest that Clostridium sp. KCTC 8440 has seven distinct CMCase genes.