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The enhancement of nuclear relaxation rates due to the interaction with a paramagnetic center (known as Paramagnetic Relaxation Enhancement) is a powerful source of structural and dynamics information, widely used in structural biology. However, many signals affected by the hyperfine interaction relax faster than the evolution periods of common NMR experiments and therefore they are broadened beyond detection. This gives rise to a so-called blind sphere around the paramagnetic center, which is a major limitation in the use of PREs. Reducing the blind sphere is extremely important in paramagnetic metalloproteins. The identification, characterization, and proper structural restraining of the first coordination sphere of the metal ion(s) and its immediate neighboring regions is key to understand their biological function. The novel HSQC scheme we propose here, that we termed R2-weighted, HSQC-AP, achieves this aim by detecting signals that escaped detection in a conventional HSQC experiment and provides fully reliable R2 values in the range of 1H R2 rates ca. 50–400 s−1. Independently on the type of paramagnetic center and on the size of the molecule, this experiment decreases the radius of the blind sphere and increases the number of detectable PREs. Here, we report the validation of this approach for the case of PioC, a small protein containing a high potential 4Fe-4S cluster in the reduced [Fe4S4]2+ form. The blind sphere was contracted to a minimal extent, enabling the measurement of R2 rates for the cluster coordinating residues.

In paramagnetic metalloproteins, longitudinal relaxation rates of 13C′ and 13Cα nuclei can be measured using 13C detected experiments and converted into electron spin-nuclear spin distance restraints, also known as Paramagnetic Relaxation Enhancement (PRE) restraints. 13C are less sensitive to paramagnetism than 1H nuclei, therefore, 13C based PREs constitute an additional, non-redundant, structural information. We will discuss the complementarity of 13C PRE restraints with 1H PRE restraints in the case of the High Potential Iron Sulfur Protein (HiPIP) PioC, for which the NMR structure of PioC has been already solved by a combination of classical and paramagnetism-based restraints. We will show here that 13C R1 values can be measured also at very short distances from the paramagnetic center and that the obtained set of 13C based restraints can be added to 1H PREs and to other classical and paramagnetism based NMR restraints to improve quality and quantity of the NMR information.

Metalloproteins play key roles across biology, and knowledge of their structure is essential to understand their physiological role. For those metalloproteins containing paramagnetic states, the enhanced relaxation caused by the unpaired electrons often makes signal detection unfeasible near the metal center, precluding adequate structural characterization right where it is more biochemically relevant. Here, we report a protein structure determination by NMR where two different sets of restraints, one containing Nuclear Overhauser Enhancements (NOEs) and another containing Paramagnetic Relaxation Enhancements (PREs), are used separately and eventually together. The protein PioC from Rhodopseudomonas palustris TIE-1 is a High Potential Iron-Sulfur Protein (HiPIP) where the [4Fe-4S] cluster is paramagnetic in both oxidation states at room temperature providing the source of PREs used as alternative distance restraints. Comparison of the family of structures obtained using NOEs only, PREs only, and the combination of both reveals that the pairwise root-mean-square deviation (RMSD) between them is similar and comparable with the precision within each family. This demonstrates that, under favorable conditions in terms of protein size and paramagnetic effects, PREs can efficiently complement and eventually replace NOEs for the structural characterization of small paramagnetic metalloproteins and de novo-designed metalloproteins by NMR. DATABASES: The 20 conformers with the lowest target function constituting the final family obtained using the full set of NMR restraints were deposited to the Protein Data Bank (PDB ID: 6XYV). The 20 conformers with the lowest target function obtained using NOEs only (PDB ID: 7A58) and PREs only (PDB ID: 7A4L) were also deposited to the Protein Data Bank. The chemical shift assignments were deposited to the BMRB (code 34487).

Nuclear magnetic resonance (NMR) spectroscopy is a key technique for the structural and functional characterization of biological molecules. This chapter introduces the reader to the basics of the technique and progresses to specific features that originate from the presence of metals and their unpaired electrons in the molecules to be analyzed. This is done in a gradual fashion to accompany the demands of characterizing increasingly complex molecules. A few strategies to illustrate how paramagnetic molecules can be studied experimentally are presented. The description of NMR spectroscopy made here is targeted towards students or researchers unfamiliar with NMR and interested in the applications of the technique relevant for biomolecular work involving metalloproteins or interactions between proteins and metal ions.

Extracellular electron transfer pathways allow bacteria to transfer electrons from the cell metabolism to extracellular substrates, such as metal oxides in natural environments and electrodes in microbial electrochemical technologies (MET). Studies of electroactive microorganisms and mainly of Shewanella oneidensis MR-1 have demonstrated that extracellular electron transfer pathways relies on several multiheme c-type cytochromes. The small tetraheme cytochrome c (STC) is highly conserved among Shewanella species and is one of the most abundant cytochromes in the periplasmic space. It transfers electrons from the cell metabolism delivered by the inner-membrane tetraheme cytochrome CymA, to the porin-cytochrome complex MtrCAB in the outer-membrane, to reduce solid electron acceptors outside the cell, or electrodes in the case of MET. In this work knock-out strains of STC of S. oneidensis MR-1, expressing STC from distinct Shewanella species were tested for their ability to perform extracellular electron transfer, allowing to explore the effect of protein mutations in living organisms. These studies, complemented by a biochemical evaluation of the electron transfer properties of the individual proteins, revealed a considerable plasticity in the molecular components involved in extracellular electron transfer. The results of this work are pioneering and of significant relevance for future rational design of cytochromes in order to enhance extracellular electron transfer and thus contribute to the practical implementation of MET.

The development of microbial electrochemical technologies (METs) rests on the deep knowledge of the extracellular electron transfer (EET) processes performed by electroactive organisms. These organisms are responsible for energy harnessing, bioremediation, and production of added-value products in these systems. It is now well recognized that multiheme c-type cytochromes (MHCs) play key roles in the processes of EET. However, given the complexity of these proteins, the understanding of the mechanisms underlying EET processes that rule microbial electroactivity requires a multidisciplinary approach that includes various areas of research, including molecular biology, biophysics, biochemistry, spectroscopy, and electrochemistry. This chapter describes the methodologies and approaches that have been used so far to explore, at the molecular level, the electron transfer processes performed by the proteins involved in EET, mainly of the MHCs, with the aim of determining the distinct aspects required for harnessing reducing power in METs.

This work was supported by the European Union’s Horizon 2020 research and innovation program under Grant 810856, National Funds Grant ERA-MBT/ 0003/2014, Ph.D. fellowship PD/BD/135187/2017 (to I. B. T.), and postdoctoral fellowships SFRH/BPD/94050/2013 and SFRH/BPD/93164/2013 (to E. M. and B. F. M.), through the FCT-Fundação para a Ciência e Tecnologia. The authors declare that they have no conflicts of interest with the contents of this article. Acknowledgments—We thank Isabel Pacheco for help in the purification of SfSIP and Dr. Américo Duarte for providing ferredoxin. We also thank all members of the Inorganic Biochemistry and NMR Laboratory for discussions and comments and feedback regarding the preparation of the manuscript. The NMR experiments were performed at CERMAX (Centro de Ressonância Magnetica António Xavier) and was financially supported by Project LISBOA-01-0145-FEDER-007660 (Microbiologia Molecular, Estrutural e Celular) funded by FEDER funds through COMPETE2020-Programa Opera-cional Competitividade e Internacionalização (POCI), the European Community’s Seventh Framework Program (FP7/2007–2013)) under Grant Agreement 283570 (BioStruct-X). Beamtime at I04 at the Diamond Light Source and assistance from the beamline staff during the synchrotron data collections are gratefully acknowledged. Siderophores make iron accessible under iron-limited conditions and play a crucial role in the survival of microorganisms. Because of their remarkable metal-scavenging properties and ease in crossing cellular envelopes, siderophores hold great potential in biotechnological applications, raising the need for a deeper knowledge of the molecular mechanisms underpinning the siderophore pathway. Here, we report the structural and functional characterization of a siderophore-interacting protein from the marine bacterium Shewanella frigidimarina NCIBM400 (SfSIP). SfSIP is a flavin-containing ferric-siderophore reductase with FAD- and NAD(P)H-binding domains that have high homology with other characterized SIPs. However, we found here that it mechanistically departs from what has been described for this family of proteins. Unlike other FAD-containing SIPs, SfSIP did not discriminate between NADH and NADPH. Furthermore, SfSIP required the presence of the Fe 2+ -scavenger, ferrozine, to use NAD(P)H to drive the reduction of Shewanella-produced hydroxamate ferric-siderophores. Additionally, this is the first SIP reported that also uses a ferredoxin as electron donor, and in contrast to NAD(P)H, its utilization did not require the mediation of ferrozine, and electron transfer occurred at fast rates. Finally, FAD oxidation was thermodynamically coupled to deprotonation at physiological pH values, enhancing the solubility of ferrous iron. On the basis of these results and the location of the SfSIP gene downstream of a sequence for putative binding of aerobic respiration control protein A (ArcA), we propose that SfSIP contributes an additional layer of regulation that maintains cellular iron homeostasis according to environmental cues of oxygen availability and cellular iron demand. publishersversion published

The gene encoding a putative siderophore-interacting protein from the marine bacterium S. frigidimarina was successfully cloned, followed by expression and purification of the gene product. Optimized crystals diffracted to 1.35 Å resolution and preliminary crystallographic analysis is promising with respect to structure determination and increased insight into the poorly understood molecular mechanisms underlying iron acquisition., Siderophore-binding proteins (SIPs) perform a key role in iron acquisition in multiple organisms. In the genome of the marine bacterium Shewanella frigidimarina NCIMB 400, the gene tagged as SFRI_RS12295 encodes a protein from this family. Here, the cloning, expression, purification and crystallization of this protein are reported, together with its preliminary X-ray crystallographic analysis to 1.35 Å resolution. The SIP crystals belonged to the monoclinic space group P21, with unit-cell parameters a = 48.04, b = 78.31, c = 67.71 Å, α = 90, β = 99.94, γ = 90°, and are predicted to contain two molecules per asymmetric unit. Structure determination by molecular replacement and the use of previously determined ∼2 Å resolution SIP structures with ∼30% sequence identity as templates are ongoing.

Plant growth and development is highly dependent on a variety of environmental conditions such as temperature, light, water availability and soil conditions that strongly affect productivity worldwide. Over the past years, several reports have raised awareness for the fact that extreme weather conditions are predicted to become more frequent in a near future, which is likely to have a strong impact in crop production. For instance, it is estimated that by 2030, global water demand solely for agriculture may have increased by more than 30% as a consequence of foreseen climate changes (Foresight, 2011). Therefore, there is an urgency to understand how plants behave when facing adverse conditions, in order to reduce productivity losses in sub-optimal environments. Plants have developed different strategies to cope with abiotic stress conditions. Upon environmental stimuli, changes in metabolism, signal transduction pathways and gene expression can be detected (Shinozaki & Yamaguchi-Shinozaki, 2007). Post-transcriptional regulatory mechanisms, as well as epigenetic and post-translational modifications, like ubiquitination and sumoylation, seem to play an important role in the regulation of gene expression in stress conditions (reviewed in Hirayama & Shinozaki, 2010). In this chapter we will provide evidences of the involvement of small RNAs (sRNAs) in the regulation of gene expression as response to abiotic stress. The role of microRNAs (miRNAs) and other sRNAs under water deficit, high salinity, cold and oxidative stress, among others, as well as their relation to hormone signalling in plants, will be reviewed. Moreover, we will show that key enzymes involved in sRNA synthesis pathways also seem to be regulated upon environmental stimuli, affecting the expression of most sRNAs and consequently of several genes.

Plant microRNAs have been implicated in various abiotic stress responses. We identified several conserved microRNAs that showed differential expression in Medicago truncatula plants subjected to water deficit: miR169 is down-regulated only in the roots and miR398a/b and miR408 are strongly up-regulated in both shoots and roots. Down-regulation of miR169 in the roots did not correlate with accumulation of its target MtHAP2-1 transcripts, suggesting that its regulation may not occur at the mRNA level or may depend on other regulatory mechanisms, which do not involve this miRNA, in water-deficit conditions. The up-regulation of miR398a/b and miR408 and the clear down-regulation of their respective target genes, which encode the copper proteins COX5b (subunit 5b of mitochondrial cytochrome c oxidase) and plantacyanin, highlight the involvement of these miRNAs in response to water deprivation in M. truncatula. Also, miR398 up-regulation is inversely correlated with the down-regulation of copper superoxide dismutase, CSD1, during water deficit. The regulation of genes encoding copper proteins by miR398a/b and miR408 suggests a link between copper homeostasis and M. truncatula adaptation to progressive water deficit.