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Pseudogene product YqiG is important for pflB expression and biohydrogen production in Escherichia coli BW25113

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Abstract

Pseudogenes in the Escherichia coli genome are assumed to be non-functional. In this study, Keio collection BW25113∆yqiG and YqiG-producing strain (BW25113/pCA24N-YqiG) were used to evaluate the importance of pseudogene yqiG in hydrogen metabolism. Our results show pseudogene protein YqiG was identified as an essential protein in the production of biohydrogen from glucose. The mutant yqiG decreased biohydrogen production from 37 µmol mg−1 protein to 6 µmol mg−1 protein compared to the wild-type strain, and glucose consumption was reduced by 80%. Through transcriptional analysis, we found that the yqiG mutation represses pflB transcription tenfold; pflB encodes pyruvate-formate lyase, one of the key enzymes in the anaerobic metabolism of E. coli. Moreover, production of YqiG stimulated glycolysis and increased biohydrogen productivity 1.5-fold compared to that of the wild-type strain. Thus, YqiG is important for the central glycolysis reaction and is able to influence hydrogen metabolism activity in E. coli.

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Acknowledgements

We express our gratitude to the National Institute of Genetics (Japan) for providing the Keio mutant and ASKA strains. The authors would like to thank the Ministry of Higher Education, Malaysia for providing Fundamental Research Grant Scheme (02-01-14-1401FR), the School of Graduate Studies, Universiti Putra Malaysia and Japan Student Services Organisation for the scholarship to Muhammad Azman Zakaria during this study.

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Authors and Affiliations

  1. Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia

    Muhammad Azman Zakaria, Mohd Zulkhairi Mohd Yusoff, Mohd Rafein Zakaria & Mohd Ali Hassan

  2. Laboratory of Biopolymer and Derivatives, Institute of Tropical Forestry and Forest Products, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia

    Mohd Zulkhairi Mohd Yusoff & Mohd Rafein Zakaria

  3. Department of Chemical Engineering and Biochemistry and Molecular Biology, Pennsylvania State University, 161 Fenske Laboratory, University Park, PA, 16802, USA

    Thomas K. Wood

  4. Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, 2-4 Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka, 808-0196, Japan

    Toshinari Maeda

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  1. Muhammad Azman Zakaria
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  2. Mohd Zulkhairi Mohd Yusoff
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  3. Mohd Rafein Zakaria
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  4. Mohd Ali Hassan
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  5. Thomas K. Wood
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  6. Toshinari Maeda
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Contributions

Study conception and design: MZMY and TM. Experiment, analysis and interpretation of data: MAZ and MZMY. Draft and revise the manuscript: MZMY, TM and MRZ. Coordinate the experiments and critical revision: MAH and TKW.

Corresponding author

Correspondence to Mohd Zulkhairi Mohd Yusoff.

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The authors declare that there have no conflict of interest in relation to this article.

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13205_2018_1461_MOESM1_ESM.pptx

Fig. S1 H2 productivity from different strains in complex glucose medium. BW25113 (plain white column), BW25113ΔyqiG (black column) and BW25113/pCA24N-YqiG (grey column). Fig. S2 Protein purification using Ni-NTA column. Overexpressed strain visualised by 10% of SDS-PAGE. Arrows indicate expected YqiG protein. Lane 1: Cell lysate, lane 2: Flow through (after bind to Ni-NTA resin), lane 3: After washing with wash buffer and 10 mM imidazole, lane 4: First washing with wash buffer and 20 mM imidazole, lane 5: Second washing with wash buffer and 20 mM imidazole, lane 6 and lane 7: Eluent wash buffer with 130 mM imidazole, and lane 8: protein marker, XL ladder. (PPTX 106 KB)

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Zakaria, M.A., Mohd Yusoff, M.Z., Zakaria, M.R. et al. Pseudogene product YqiG is important for pflB expression and biohydrogen production in Escherichia coli BW25113. 3 Biotech 8, 435 (2018). https://doi.org/10.1007/s13205-018-1461-2

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