Next-generation Sequencing-based Transcriptome Analysis of L-lysine-producing Corynebacterium Glutamicum ATCC 21300 Strain

Overview

Journal J Microbiol

Specialty Microbiology

Date 2014 Jan 4

PMID 24385368

Citations 4

Authors

Hong-Il Kim

Jae-Young Nam

Jae-Yong Cho

Chang-Soo Lee

Young-Jin Park

Affiliations

Soon will be listed here.

Abstract

In the present study, 151 genes showed a significant change in their expression levels in Corynebacterium glutamicum ATCC 21300 compared with those of C. glutamicum ATCC 13032. Of these 151 genes, 56 genes (2%) were up-regulated and 95 genes (3%) were down-regulated. RNA sequencing analysis also revealed that 11 genes, involved in the L-lysine biosynthetic pathway of C. glutamicum, were up- or down-regulated compared with those of C. glutamicum ATCC 13032. Of the 151 genes, 10 genes were identified to have mutations including SNP (9 genes) and InDel (1 gene). This information will be useful for genome breeding of C. glutamicum to develop an industrial amino acid-producing strain with minimal mutation.

Citing Articles

Review of the Proteomics and Metabolic Properties of .

Park J, Lim S Microorganisms. 2024; 12(8).

PMID: 39203523 PMC: 11356982. DOI: 10.3390/microorganisms12081681.

Transcriptome analysis of L-leucine-producing Corynebacterium glutamicum under the addition of trimethylglycine.

Wang J, Wang X, Liang Q, Li D, Li D, Guo Q Amino Acids. 2021; 54(2):229-240.

PMID: 34837555 DOI: 10.1007/s00726-021-03105-5.

Comparative analysis of the Corynebacterium glutamicum transcriptome in response to changes in dissolved oxygen levels.

Liu X, Yang S, Wang F, Dai X, Yang Y, Bai Z J Ind Microbiol Biotechnol. 2016; 44(2):181-195.

PMID: 27844170 DOI: 10.1007/s10295-016-1854-3.

Transcriptome and Gene Ontology (GO) Enrichment Analysis Reveals Genes Involved in Biotin Metabolism That Affect L-Lysine Production in Corynebacterium glutamicum.

Kim H, Kim J, Park Y Int J Mol Sci. 2016; 17(3):353.

PMID: 27005618 PMC: 4813214. DOI: 10.3390/ijms17030353.

References

Koffas M, Jung G, Aon J, Stephanopoulos G . Effect of pyruvate carboxylase overexpression on the physiology of Corynebacterium glutamicum. Appl Environ Microbiol. 2002; 68(11):5422-8. PMC: 129921. DOI: 10.1128/AEM.68.11.5422-5428.2002. View

Schiel B, Wendisch V, Katsoulidis E, Mockel B, Sahm H, Eikmanns B . Pyruvate carboxylase is a major bottleneck for glutamate and lysine production by Corynebacterium glutamicum. J Mol Microbiol Biotechnol. 2001; 3(2):295-300. View

Jahn C, Charkowski A, Willis D . Evaluation of isolation methods and RNA integrity for bacterial RNA quantitation. J Microbiol Methods. 2008; 75(2):318-24. DOI: 10.1016/j.mimet.2008.07.004. View

Moritz B, Striegel K, De Graaf A, Sahm H . Kinetic properties of the glucose-6-phosphate and 6-phosphogluconate dehydrogenases from Corynebacterium glutamicum and their application for predicting pentose phosphate pathway flux in vivo. Eur J Biochem. 2000; 267(12):3442-52. DOI: 10.1046/j.1432-1327.2000.01354.x. View

Loos A, Glanemann C, Willis L, OBrien X, Lessard P, Gerstmeir R . Development and validation of corynebacterium DNA microarrays. Appl Environ Microbiol. 2001; 67(5):2310-8. PMC: 92872. DOI: 10.1128/AEM.67.5.2310-2318.2001. View

Ikeda M, Nakagawa S . The Corynebacterium glutamicum genome: features and impacts on biotechnological processes. Appl Microbiol Biotechnol. 2003; 62(2-3):99-109. DOI: 10.1007/s00253-003-1328-1. View

Lee C, Nam J, Son E, Kwon O, Han W, Cho J . Next-generation sequencing-based genome-wide mutation analysis of L-lysine-producing Corynebacterium glutamicum ATCC 21300 strain. J Microbiol. 2012; 50(5):860-3. DOI: 10.1007/s12275-012-2109-2. View

Ikeda M, Ohnishi J, Hayashi M, Mitsuhashi S . A genome-based approach to create a minimally mutated Corynebacterium glutamicum strain for efficient L-lysine production. J Ind Microbiol Biotechnol. 2006; 33(7):610-5. DOI: 10.1007/s10295-006-0104-5. View

Muffler A, Bettermann S, Haushalter M, Horlein A, Neveling U, Schramm M . Genome-wide transcription profiling of Corynebacterium glutamicum after heat shock and during growth on acetate and glucose. J Biotechnol. 2002; 98(2-3):255-68. DOI: 10.1016/s0168-1656(02)00136-0. View

10.

Sahm H, Eggeling L, De Graaf A . Pathway analysis and metabolic engineering in Corynebacterium glutamicum. Biol Chem. 2000; 381(9-10):899-910. DOI: 10.1515/BC.2000.111. View

11.

Ohnishi J, Mitsuhashi S, Hayashi M, Ando S, Yokoi H, Ochiai K . A novel methodology employing Corynebacterium glutamicum genome information to generate a new L-lysine-producing mutant. Appl Microbiol Biotechnol. 2002; 58(2):217-23. DOI: 10.1007/s00253-001-0883-6. View

12.

Cox M, Peterson D, Biggs P . SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics. 2010; 11:485. PMC: 2956736. DOI: 10.1186/1471-2105-11-485. View

13.

Hartmann M, Tauch A, Eggeling L, Bathe B, Mockel B, Puhler A . Identification and characterization of the last two unknown genes, dapC and dapF, in the succinylase branch of the L-lysine biosynthesis of Corynebacterium glutamicum. J Biotechnol. 2003; 104(1-3):199-211. DOI: 10.1016/s0168-1656(03)00156-1. View