Deconstructing the Dissimilatory Sulfate Reduction Pathway: Isotope Fractionation of a Mutant Unable of Growth on Sulfate

Abstract

The sulfur isotope record provides key insight into the history of Earth's redox conditions. A detailed understanding of the metabolisms driving this cycle, and specifically microbial sulfate reduction (MSR), is crucial for accurate paleoenvironmental reconstructions. This includes a precise knowledge of the step-specific sulfur isotope effects during MSR. In this study, we aim at resolving the cellular-level fractionation factor during dissimilatory sulfite reduction to sulfide within MSR, and use this measured isotope effect as a calibration to enhance our understanding of the biochemistry of sulfite reduction. For this, we merge measured isotope effects associated with dissimilatory sulfite reduction with a quantitative model that explicitly links net fractionation, reaction reversibility, and intracellular metabolite levels. The highly targeted experimental aspect of this study was possible by virtue of the availability of a deletion mutant strain of the model sulfate reducer Desulfovibrio vulgaris (strain Hildenborough), in which the sulfite reduction step is isolated from the rest of the metabolic pathway owing to the absence of its QmoABC complex (ΔQmo). This deletion disrupts electron flux and prevents the reduction of adenosine phosphosulfate (APS) to sulfite. When grown in open-system steady-state conditions at 10% maximum growth rate in the presence of sulfite and lactate as electron donor, sulfur isotope fractionation factors averaged −15.9‰ (1 σ = 0.4), which appeared to be statistically indistinguishable from a pure enzyme study with dissimilatory sulfite reductase. We coupled these measurements with an understanding of step-specific equilibrium and kinetic isotope effects, and furthered our mechanistic understanding of the biochemistry of sulfite uptake and ensuing reduction. Our metabolically informed isotope model identifies flavodoxin as the most likely electron carrier performing the transfer of electrons to dissimilatory sulfite reductase. This is in line with previous work on metabolic strategies adopted by sulfate reducers under different energy regimes, and has implications for our understanding of the plasticity of this metabolic pathway at the center of our interpretation of modern and palaeo-environmental records.

Proteomic and Isotopic Response of Desulfovibrio vulgaris to DsrC Perturbation

“…Recent modeling studies have attempted to describe these relationships under all environmental conditions and as a consequence of the inherent enzymatic steps, each of which may express an isotope fractionation (Bradley et al, 2011; Wing and Halevy, 2014; Bradley et al, 2016; Wenk et al, 2017). A few experimental studies have examined the potential role of intermediate S species on fractionation on net S isotopic fractionation (Smock et al, 1998; Leavitt et al, 2014; Bertran et al, 2018b), as have some model studies (Rees, 1973; Brunner and Bernasconi, 2005; Farquhar et al, 2007; Johnston et al, 2007; Turchyn et al, 2010; Brunner et al, 2012; Bertran et al, 2018a). Other studies have examined fractionation imposed by the individual enzymes, such as DsrAB (Leavitt et al, 2015) or AprAB (Sim et al, 2019) or highlighted the importance of material fluxes of sulfur through the most up-to-date MSR metabolic network (Bradley et al, 2016).…”

Microbial diversity and sulfur cycling in an early earth analogue: From ancient novelty to modern commonality

“…Sulfate-reducing organisms are the most prevalent component of the reductive sulfur cycle in most marine and aquatic ecosystems. Aspects of the ecology 2 , physiology 39 , and biochemistry 40,41,42 of dissimilatory sulfate reduction have been extensively investigated 43 .…”

Expanded Genomic Sampling Refines Current Understanding of the Distribution and Evolution of Sulfur Metabolisms in the Desulfobulbales

“…The knowledge gap here resides with our understanding of MSD, as MSR has been far more thoroughly studied ( Fry et al, 1986 ; LeGall and Fauque, 1988 ; Habicht and Canfield, 1998 ; Canfield, 2001 ; Shen et al, 2001 ; Habicht et al, 2002 ; Zane et al, 2010 ; Keller and Wall, 2011 ; Pereira et al, 2011 ; Leavitt et al, 2013 ; Parey et al, 2013 ; Wing and Halevy, 2014 ; Fike et al, 2015 ; Bradley et al, 2016 ; Bertran et al, 2018 ). That is, the true diversity and ecological distribution of sulfur disproportionation is still unknown owing to the lack of a unique enzymatic and genetic marker.…”