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PROVIDER: PRJNA933380 | ENA |
REPOSITORIES: ENA
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Project description:Chitinibacter sp. SCUT-21 isolate:SCUT-21 Genome sequencing
| PRJNA866669 | ENA
Project description:Investigation of whole genome gene expression level changes in Streptomyces sp. SirexAA-E (ActE) when grown on different carbon sources. The results of this study demonstrate that ActE upregulates a small number of genes specific for the utilization of the avaliable carbon source. Cellulolytic Streptomyces sp. SirexAA-E (ActE), isolated from the pinewood-boring wasp Sirex noctilio, has a genome enriched for biomass utilization. The secreted proteomes obtained from growth on pure polysaccharides catalyzed hydrolysis of cellulose, mannan, and xylan with specific activities comparable to Spezyme CP, a commercial cellulase preparation. During reaction of an ActE secretome with cellulose, reducing sugar release was markedly stimulated in the presence of O2. ActE also expresses and secretes an expanded repertoire of enzymes during growth on natural and pre-treated biomass. These results indicate a new microbial contribution to biomass utilization that is widely distributed in natural environments by insects Streptomyces sp. ActE was grown in minimal medium supplimented with 0.5% carbon source (glucose, sigmacell-20, xylan, chitin, cellobiose, or AFEX). Cells were grown for 7 days and total RNA was extracted from the cell pellet. At least 3 biological replicates were performed for each carbon source (glucose, 3; sigmacell, 3; xylan, 5; chitin, 3; cellobiose 3; AFEX 3). Each biological replicate contained 3 technical replicates. The complete dataset were RMA Background Corrected, quantile normalized, the RMA algorithm was utilized by DNAStar ArrayStar.
2013-12-31 | E-GEOD-31748 | biostudies-arrayexpress
Project description:Chitin utilization by microbes plays a significant role in cycling of carbon and nitrogen in the biosphere, and the study of the microbial approaches used to degrade chitin will facilitate our understanding of bacterial strategies to degrade this recalcitrant polysaccharide. The early stages of chitin depolymerization by the bacterium Cellvibrio japonicus have been characterized and are dependent on one chitin-specific lytic polysaccharide monooxygenase and non-redundant glycoside hydrolases from the family GH18 to generate chito-oligosaccharides for entry into metabolism. Here, we describe the mechanisms for the latter stages of chitin utilization by C. japonicus with an emphasis on the fate of chito-oligosaccharides. Our systems biology approach combined transcriptomics, bacterial genetics, and complex environmental substrates to determine the essential mechanisms for chito-oligosaccharide transport and catabolism in Cellvibrio japonicus. Using RNAseq analysis we found not only the up-regulation of genes that encode CAZymes specific for chitin metabolism but also a coordinated expression of non-chitin specific CAZyme genes. Furthermore, we used mutational analysis to characterize the hex20B gene product, predicted to encode a hexosaminidase, and found that it is required for efficient utilization of chito-oligosaccharides. Surprisingly, two additional gene loci (CJA_0353 and CJA_1157), which encode putative TonB-dependent transporters, were essential for shuttling chito-oligosaccharides into the periplasmic space. Here we propose naming these loci cttA (chito-oligosaccharides transporter A) and cttB respectively. This study further develops our model of how C. japonicus can derive nutrients from recalcitrant chitin-containing substrates and may be potentially useful for other environmentally or industrially important bacteria.
2020-04-30 | GSE149593 | GEO
Project description:Understanding the strategies used by bacteria to degrade polysaccharides constitutes an invaluable tool for biotechnological applications Bacteria are major mediators of polysaccharide degradation in nature, however the complex mechanisms used to detect, degrade, and consume these substrates are not well understood, especially for recalcitrant polysaccharides such as chitin It has been previously shown that the model bacterial saprophyte Cellvibrio japonicus is able to catabolize chitin, but little is known about the enzymatic machinery underlying this capability Previous analyses of the C japonicus genome and proteome indicated the presence of four family 18 Glycoside Hydrolase (GH18) enzymes, and studies of the proteome indicated that all are involved in chitin utilization Using a combination of in vitro and in vivo approaches, we have studied the roles of these four chitinases in chitin bioconversion Genetic analyses showed that only the chi18D gene product is essential for the degradation of chitin substrates Biochemical characterization of the four enzymes showed functional differences and synergistic effects during chitin degradation, indicating non-redundant roles in the cell Transcriptomic studies revealed complex regulation of the chitin degradation machinery of C japonicus and confirmed the importance of CjChi18D and CjLPMO10A, a previously characterized chitin-active enzyme With this systems biology approach, we deciphered the physiological relevance of the GH18 enzymes for chitin degradation in C japonicus, and the combination of in vitro and in vivo approaches provided a comprehensive understanding of the initial stages of chitin degradation by this bacterium
2018-01-24 | GSE108935 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE3101: Chitin oligosaccharide induction GSE3102: Crab shell attachment GSE3103: Chitin sensor Abstract: Chitin, an insoluble polymer of GlcNAc, is an abundant source of carbon, nitrogen, and energy for marine microorganisms. Microarray expression profiling and mutational studies of Vibrio cholerae growing on a natural chitin surface, or with the soluble chitin oligosaccharides (GlcNAc)(2-6), GlcNAc, or the glucosamine dimer (GlcN)2 identified three sets of differentially regulated genes. We show that (i) ChiS, a sensor histidine kinase, regulates expression of the (GlcNAc)(2-6) gene set, including a (GlcNAc)2 catabolic operon, two extracellular chitinases, a chitoporin, and a PilA-containing type IV pilus, designated ChiRP (chitin-regulated pilus) that confers a significant growth advantage to V. cholerae on a chitin surface; (ii) GlcNAc causes the coordinate expression of genes involved with chitin chemotaxis and adherence and with the transport and assimilation of GlcNAc; (iii) (GlcN)2 induces genes required for the transport and catabolism of nonacetylated chitin residues; and (iv) the constitutively expressed MSHA pilus facilitates adhesion to the chitin surface independent of surface chemistry. Collectively, these results provide a global portrait of a complex, multistage V. cholerae program for the efficient utilization of chitin. Refer to individual Series
2006-03-07 | E-GEOD-4388 | biostudies-arrayexpress
Project description:Abstract: Chitin, an insoluble polymer of GlcNAc, is an abundant source of carbon, nitrogen, and energy for marine microorganisms. Microarray expression profiling and mutational studies of Vibrio cholerae growing on a natural chitin surface, or with the soluble chitin oligosaccharides (GlcNAc)(2-6), GlcNAc, or the glucosamine dimer (GlcN)2 identified three sets of differentially regulated genes. We show that (i) ChiS, a sensor histidine kinase, regulates expression of the (GlcNAc)(2-6) gene set, including a (GlcNAc)2 catabolic operon, two extracellular chitinases, a chitoporin, and a PilA-containing type IV pilus, designated ChiRP (chitin-regulated pilus) that confers a significant growth advantage to V. cholerae on a chitin surface; (ii) GlcNAc causes the coordinate expression of genes involved with chitin chemotaxis and adherence and with the transport and assimilation of GlcNAc; (iii) (GlcN)2 induces genes required for the transport and catabolism of nonacetylated chitin residues; and (iv) the constitutively expressed MSHA pilus facilitates adhesion to the chitin surface independent of surface chemistry. Collectively, these results provide a global portrait of a complex, multistage V. cholerae program for the efficient utilization of chitin. This SuperSeries is composed of the SubSeries listed below.
2006-03-08 | GSE4388 | GEO
Project description:Proteomes of Vibrio sp. 1A01 exponentially growing on various carbon sources as well as on chitin. Chitin samples contain planktonic cells, particle-associated proteins and excreted proteins.
2022-05-19 | MSV000089499 | MassIVE