Genome-Wide Analyses of Proteome and Acetylome in Zymomonas mobilis Under N2-Fixing Condition.

Ayesha Nisar,Yuhuan Huang,Mingxiong He,Xiangxu Gongye,Sawar Khan,Mao Chen,Bo Wu

doi:10.3389/fmicb.2021.740555

Abstract

Zymomonas mobilis, a promising candidate for industrial biofuel production, is capable of nitrogen fixation naturally without hindering ethanol production. However, little is known about the regulation of nitrogen fixation in Z. mobilis. We herein conducted a high throughput analysis of proteome and protein acetylation in Z. mobilis under N2-fixing conditions and established its first acetylome. The upregulated proteins mainly belong to processes of nitrogen fixation, motility, chemotaxis, flagellar assembly, energy production, transportation, and oxidation–reduction. Whereas, downregulated proteins are mainly related to energy-consuming and biosynthetic processes. Our acetylome analyses revealed 197 uniquely acetylated proteins, belonging to major pathways such as nitrogen fixation, central carbon metabolism, ammonia assimilation pathway, protein biosynthesis, and amino acid metabolism. Further, we observed acetylation in glycolytic enzymes of central carbon metabolism, the nitrogenase complex, the master regulator NifA, and the enzyme in GS/GOGAT cycle. These findings suggest that protein acetylation may play an important role in regulating various aspects of N2-metabolism in Z. mobilis. This study provides new knowledge of specific proteins and their associated cellular processes and pathways that may be regulated by protein acetylation in Z. mobilis.

Highlights

Nitrogen fixation in free-living diazotrophic bacteria is regulated at diverse levels, including transcriptional regulation by nitrogen-fixing island (NifA) and its regulator NifL (Dixon, 1998; Lei et al, 1999; Schmitz et al, 2002; Martinez-Argudo et al, 2004b; Perry et al, 2005), post-transcriptional regulation by non-coding RNAs (Wang et al, 2009; Zhan et al, 2016, 2019), translational regulation by a conformational switch in NifL (Martinez-Argudo et al, 2004a), and various post-translational modifications (PTMs)
The genome-wide proteome analyses revealed that upregulated proteins were mostly involved in processes such as nitrogen fixation, motility, chemotaxis, flagellar assembly, energy production, transportation, and oxidation–reduction (Figures 2, 3)
Since nitrogen fixation is a costly process that requires a supply of ATP and reducing power (Yan et al, 2010; Varley et al, 2015; Suyal et al, 2017), it is reasonable that the proteins involved in energy production or oxidation–reduction were upregulated under nitrogen fixation

Summary

Introduction

A Gram-negative facultative anaerobic bacterium, is a promising candidate for industrial biofuel production with a suite of desirable characteristics (Doelle et al, 1993; Sprenger, 1996; Kalnenieks, 2006; Panesar et al, 2006; Bai et al, 2008; Yang et al, 2009, 2016; He et al, 2014; Martien et al, 2019; Todhanakasem et al, 2020). In comparison with other free-living diazotrophic bacteria, Z. mobilis has just a Mo-dependent nitrogen-fixing system. Aside from the conserved genetic structure of the nitrogenfixing island, it is very important to decipher the regulatory mechanisms underlying the nitrogen fixation. This will help to better understand nitrogen fixation but is crucial for developing more efficient nitrogen-fixing pathways. Such novel pathways will help in reducing the use of chemical fertilizers and replacing the nitrogen source in the fermentation industry. Nitrogen fixation is regulated by sensing oxygen, ammonium, cofactors, or signal messengers (Dixon and Kahn, 2004; Masepohl and Hallenbeck, 2010; Xie et al, 2010; Zhang et al, 2012; Hoffmann et al, 2015)

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Discussion

Conclusion