The genome sequence of the ethanologenic bacterium  Zymomonas mobilis  ZM4

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Abstract

We report the complete genome sequence of Zymomonas mobilis ZM4 (ATCC31821), an ethanologenic microorganism of interest for the production of fuel ethanol. The genome consists of 2,056,416 base pairs forming a circular chromosome with 1,998 open reading frames (ORFs) and three ribosomal RNA transcription units. The genome lacks recognizable genes for 6-phosphofructokinase, an essential enzyme in the Embden-Meyerhof-Parnas pathway, and for two enzymes in the tricarboxylic acid cycle, the 2-oxoglutarate dehydrogenase complex and malate dehydrogenase, so glucose can be metabolized only by the Entner-Doudoroff pathway. Whole genome microarrays were used for genomic comparisons with the Z. mobilis type strain ZM1 (ATCC10988) revealing that 54 ORFs predicted to encode for transport and secretory proteins, transcriptional regulators and oxidoreductase in the ZM4 strain were absent from ZM1. Most of these ORFs were also found to be actively transcribed in association with ethanol production by ZM4.

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The online version of this article (doi:10.1038/nbt1045) contains supplementary material, which is available to authorized users.

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To examine the utility and performance of 50mer oligonucleotide (oligonucleotide probe) microarrays, gene-specific oligonucleotide probes were spotted along with PCR probes onto glass microarrays and the performance of each probe type was evaluated. The specificity of oligonucleotide probes was studied using target RNAs that shared various degrees of sequence similarity. Sensitivity was defined as the ability to detect a 3-fold change in mRNA. No significant difference in sensitivity between oligonucleotide probes and PCR probes was observed and both had a minimum reproducible detection limit of approximately 10 mRNA copies/cell. Specificity studies showed that for a given oligonucleotide probe any 'non-target' transcripts (cDNAs) >75% similar over the 50 base target may show cross-hybridization. Thus non-target sequences which have >75-80% sequence similarity with target sequences (within the oligonucleotide probe 50 base target region) will contribute to the overall signal intensity. In addition, if the 50 base target region is marginally similar, it must not include a stretch of complementary sequence >15 contiguous bases. Therefore, knowledge about the target sequence, as well as its similarity to other mRNAs in the target tissue or RNA sample, is required to design successful oligonucleotide probes for quality microarray results. Together these results validate the utility of oligonucleotide probe (50mer) glass microarrays.

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Author and article information

Contributors

Jeong-Sun Seo: jeongsun@macrogen.com

Hyen Sam Kang: khslab@snu.ac.kr

Journal

Journal ID (nlm-ta): Nat Biotechnol

Journal ID (iso-abbrev): Nat. Biotechnol

Title: Nature Biotechnology

Publisher: Nature Publishing Group US (New York )

ISSN (Print): 1087-0156

ISSN (Electronic): 1546-1696

Publication date (Electronic): 12 December 2004

Publication date PMC-release: 12 December 2004

Publication date (Print): 2005

Volume: 23

Issue: 1

Pages: 63-68

Affiliations

[1 ]GRID grid.492507.d, ISNI 0000 0004 6379 344X, Macrogen Inc., World Meridian Venture Center, 60-24, Gasan-dong, ; Seoul, 153-781 Korea

[2 ]GRID grid.31501.36, ISNI 0000 0004 0470 5905, Department of Biochemistry and Ilchun Molecular Medicine Institute, , Medical Research Center, College of Medicine, Seoul National University, ; Seoul, 110-799 Korea

[3 ]GRID grid.31501.36, ISNI 0000 0004 0470 5905, Department of Microbiology, , School of Biological Sciences, Seoul National University, ; Seoul, 151-742 Korea

[4 ]GRID grid.255649.9, ISNI 0000 0001 2171 7754, Department of Computer Science, , Ewha Womans University, ; Seoul, 120-750 Korea

Article

Publisher ID: BFnbt1045

DOI: 10.1038/nbt1045

PMC ID: 6870993

PubMed ID: 15592456

SO-VID: 1d05a64e-6f93-47cb-9022-25f0e920e8bc

License:

This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike license ( http://creativecommons.org/licenses/by-nc-sa/3.0/), which permits distribution, and reproduction in any medium, provided the original author and source are credited. This license does not permit commercial exploitation, and derivative works must be licensed under the same or similar license.

History

Date received : 28 June 2004

Date accepted : 6 October 2004

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ScienceOpen disciplines: Biotechnology

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ScienceOpen disciplines: Biotechnology

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The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4

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Abstract

Supplementary information

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Genome Engineering using CRISPR

Most cited references 30

Consed:A Graphical Tool for Sequence Finishing

Metabolic Engineering of a Pentose Metabolism Pathway in Ethanologenic Zymomonas mobilis.

Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays.

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