Divergence of plastid 2-oxoglutarate “only” transporters away from general transporters by using a cysteine-rich architecture

D Gunawardana

doi:10.4038/sljb.v6i2.81

Abstract

The common carbon and nitrogen currency, 2-oxoglutarate, could become a valuable resource for nitrogen assimilation and carbon centered biochemical fates. Here in this in silico study, a myriad of factors was used, namely phylogeny, sequence comparisons, and presence and location of clustered cysteines in specific plastid transporters of 2-oxoglutarate, to examine their evolution away from more generalized transporters. This transition would be to adopt the capability of internalizing 2-oxoglutarate alone or with superior specificities at the expense of malate. In phylogeny, the specific 2-oxoglutarate transporters (Cluster 1) are clustered in a separate clade away from 2 clades of general transporters (Cluster 2 and 3). The exclusivity (Cluster 1) and promiscuity of transporters (Cluster 2 and 3) compared to Arabidopsis counterparts characterized prior to this study, were used as a benchmark for my study. Within this mother clade of exclusive transporters, C4 and C3 2-oxoglutarate transporters once again form separate clusters of monophyly. Furthermore, a pattern of Cys –X-X-Cys-X(19)-Cys is conserved within the 2-oxo-glutarate only transporters that is missing in general transporters. Cysteines which are functionally key residues are inferred to be mediating intra- or inter-reactive disulfide bond formation or using a thiol (sulfhydryl) group for transport or to be forming a metal binding site. When a disulfide bond prediction tool was employed, it showed with negligible doubt that the Cys-X-X Cys-X(19) -Cys region was a strong contender for 2 separate disulfide bonds, although the middle cysteine was predicted to be involved in both. In addition, Cluster 2 general Zea mays C4 transporters are shown to be more recalcitrant to mutations of cysteines, compared to Panicum and Oryza counterparts. The study of 2-oxoglutarate and its availability in the chloroplast could play a two-prong role in C4 plants: to be a candidate for synthesis of bundle sheath cell Rubisco enzyme, which makes up ~50% of plant proteins, via ammonia assimilation, and even playing a role in carbon-centered biochemical pathways. This study could greatly facilitate choices in the tinkering of the right transporters for a future C4 rice in a climate change impacted world.

Highlights

There are two main global divisions in relation to flowering plants; dicot versus monocot and C3 against C4 photosynthesis. The former has been estimated to have taken place between 150-140 Mya, while the latter division is suggested to have taken place between 35-32 Mya (Chaw et al, 2004; Christin et al, 2008). The former can be corroborated by key anatomical features, and the latter has structural (Kranz anatomy, single cell C4 photosynthesis etc), physiological and biochemical
The Arabidopsis AtpOmt1 protein was found as a divergent node in phylogeny that deviated prior to the emergence of C4 photosynthesis and clustered with 6 Oryza (C3), 3 Zea (C4) and 4 Panicum (C4) proteins as a monophyletic clade (Figure 2)
The phylogeny of unique 2-oxoglutarate only transporters suggests that C3 and C4 photosynthesis-based divisions share the same cysteine architecture perhaps alluding to common shared functionality

Summary

Introduction

There are two main global divisions in relation to flowering plants; dicot versus monocot and C3 against C4 photosynthesis The former has been estimated to have taken place between 150-140 Mya, while the latter division is suggested to have taken place between 35-32 Mya (Chaw et al, 2004; Christin et al, 2008). Gases and has independently evolved in at least 65 occasions, which consolidates the emergence and reemergence of a convergent evolutionary fate With this in mind, there is a worldwide effort to transform the staple of Asia - the domesticated genus Oryza from a C3 engine into a supercharged C4 photosynthetic system where CO2 will be concentrated at the Rubisco (Ribulose 1-, 5Bisphosphate Carboxylase) active site (Zhu et al, 2010; Feldman et al, 2014)

Methods

Results

Conclusion