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Understanding metabolic adaptation by using bacterial laboratory evolution and trans-omics analysis.

ABSTRACT: Many diseases such as metabolic syndrome, cancer, inflammatory diseases, and pathological phenomena can be understood as an adaptive reconstitution of the metabolic state (metabolic adaptation). One of the effective approaches to reveal the property of metabolic networks is using model organisms such as microorganisms that are easier to experiment with than higher organisms. Using the laboratory evolution approach, we can elucidate the evolutionary dynamics in various stress environments, which provide us an understanding of the metabolic adaptation. In addition, the integration of omics data and phenotypic data enables us to clarify the genetic and phenotypic alterations during adaptation. In this review, we describe our recent studies on bacterial laboratory evolution and the omics approach to clarify the stress adaptation process. We have also obtained high-dimensional phenotypic data using our automated culture system. By combining these genomic and transcriptomic data within high-throughput phenotypic data, we can discuss the complex trans-omics network of metabolic adaptation.

SUBMITTER: Horinouchi T

PROVIDER: S-EPMC7311587 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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Understanding metabolic adaptation by using bacterial laboratory evolution and trans-omics analysis.

Horinouchi Takaaki T Furusawa Chikara C

Biophysical reviews 20200511 3

Many diseases such as metabolic syndrome, cancer, inflammatory diseases, and pathological phenomena can be understood as an adaptive reconstitution of the metabolic state (metabolic adaptation). One of the effective approaches to reveal the property of metabolic networks is using model organisms such as microorganisms that are easier to experiment with than higher organisms. Using the laboratory evolution approach, we can elucidate the evolutionary dynamics in various stress environments, which ...[more]

PMID: 32394353

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Project description:Background:Biosynthesis of sabinene, a bicyclic monoterpene, has been accomplished in engineered microorganisms by introducing heterologous pathways and using renewable sugar as a carbon source. However, the efficiency and titers of this method are limited by the low host tolerance to sabinene (in both eukaryotes and prokaryotes). Results:In this study, Escherichia coli BL21(DE3) was selected as the strain for adaptive laboratory evolution. The strain was evolved by serial passaging in the medium supplemented with gradually increasing concentration of sabinene, and the evolved strain XYF(DE3), which exhibited significant tolerance to sabinene, was obtained. Then, XYF(DE3) was used as the host for sabinene production and an 8.43-fold higher sabinene production was achieved compared with the parental BL21(DE3), reaching 191.76 mg/L. Whole genomes resequencing suggested the XYF(DE3) strain is a hypermutator. A comparative analysis of transcriptomes of XYF(DE3) and BL21(DE3) was carried out to reveal the mechanism underlying the improvement of sabinene tolerance, and 734 up-regulated genes and 857 down-regulated genes were identified. We further tested the roles of the identified genes in sabinene tolerance via reverse engineering. The results demonstrated that overexpressions of ybcK gene of the DLP12 family, the inner membrane protein gene ygiZ, and the methylmalonyl-CoA mutase gene scpA could increase sabinene tolerance of BL21(DE3) by 127.7%, 71.1%, and 75.4%, respectively. Furthermore, scanning electron microscopy was applied to monitor cell morphology. Under sabinene stress, the parental BL21(DE3) showed increased cell length, whereas XYF(DE3) showed normal cell morphology. In addition, overexpression of ybcK, ygiZ or scpA could partially rescue cell morphology under sabinene stress and overexpression of ygiZ or scpA could increase sabinene production in BL21(DE3). Conclusions:This study not only obtained a sabinene-tolerant strain for microbial production of sabinene but also revealed potential regulatory mechanisms that are important for sabinene tolerance. In addition, for the first time, ybcK, ygiZ, and scpA were identified to be important for terpene tolerance in E. coli BL21(DE3).

Project description:Cyclooxygenase 2 (COX-2) is involved in the initial steps of colorectal cancer (CRC) formation, playing a key role in the catalysis of arachidonic acid to prostaglandin E2 (PGE2). The human telomerase reverse transcriptase (hTERT or TERT) also plays an important role in colorectal cancer growth, conferring sustained cell proliferation and survival. Although hTERT induces COX-2 expression in gastric and cervical cancer, their interaction has not been investigated in the context of CRC. COX-2, PGE2 levels, and telomerase activity were evaluated by immunohistochemistry, ELISA, and TRAP assay in 49 colorectal cancer samples. PTGS1, PTGS2, PTGES3, TERT mRNA, and protein levels were investigated using RNA-seq and antibody-based protein profiling data from the TCGA and HPA projects. A multi-omics comparison was performed between PTGS2 and TERT, using RNAseq, DNA methylation, copy number variations (CNVs), single nucleotide polymorphisms (SNPs), and insertions/deletions (Indels) data. COX-2 expression was positive in 40/49 CRCs, bearing cytoplasmic and heterogeneous staining, from moderate to high intensity. COX-2 staining was mainly detected in the stroma of the tumor cells and the adjacent normal tissues. PGE2 expression was lower in CRC compared to the adjacent normal tissue, and inversely correlated to telomerase activity in right colon cancers. COX-1 and COX-2 were anticorrelated with TERT. Isoform structural analysis revealed the most prevalent transcripts driving the differential expression of PTGS1, PTGS2, PTGES3, and TERT in CRC. COX-2 expression was significantly higher among B-Raf proto-oncogene, serine/threonine kinase, mutant (BRAFmut) tumors. Kirsten ras oncogene (KRAS) mutations did not affect COX-2 or TERT expression. The promoter regions of COX-2 and TERT were reversely methylated. Our data support that COX-2 is involved in the early stages of colorectal cancer development, initially affecting the tumor's stromal microenvironment, and, subsequently, the epithelial cells. They also highlight an inverse correlation between COX-2 expression and telomerase activity in CRC, as well as differentially methylated patterns within the promoter regions of COX-2 and TERT.

Dataset Information

Understanding metabolic adaptation by using bacterial laboratory evolution and trans-omics analysis.

Publications

Understanding metabolic adaptation by using bacterial laboratory evolution and trans-omics analysis.

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