Stepwise pathway for early evolutionary assembly of dissimilatory sulfite and sulfate reduction

Funding Information: FLS and SN acknowledge support from the Wiener Wissenschafts, Forschungs- und Technologiefonds (Austria) through the grant VRG15-007. FLS gratefully acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation program (grant agreement 803768). IACP acknowledges support from Fundação para a Ciência e Tecnologia (Portugal) through grants PTDC/BIA-MIC/6512/2014 and PTDC/BIA-BQM/29118/2017, R&D unit MOSTMICRO-ITQB (UIDB/04612/2020 and UIDP/04612/2020), and LS4FUTURE Associated Laboratory (LA/P/0087/2020). The computational results of this work have been achieved using the Life Science Compute Cluster (LiSC) of the University of Vienna. Funding Information: FLS and SN acknowledge support from the Wiener Wissenschafts, Forschungs- und Technologiefonds (Austria) through the grant VRG15-007. FLS gratefully acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation program (grant agreement 803768). IACP acknowledges support from Fundação para a Ciência e Tecnologia (Portugal) through grants PTDC/BIA-MIC/6512/2014 and PTDC/BIA-BQM/29118/2017, R&D unit MOSTMICRO-ITQB (UIDB/04612/2020 and UIDP/04612/2020), and LS4FUTURE Associated Laboratory (LA/P/0087/2020). The computational results of this work have been achieved using the Life Science Compute Cluster (LiSC) of the University of Vienna. Publisher Copyright: © 2023, The Author(s).Microbial dissimilatory sulfur metabolism utilizing dissimilatory sulfite reductases (Dsr) influenced the biochemical sulfur cycle during Earth’s history and the Dsr pathway is thought to be an ancient metabolic process. Here we performed comparative genomics, phylogenetic, and synteny analyses of several Dsr proteins involved in or associated with the Dsr pathway across over 195,000 prokaryotic metagenomes. The results point to an archaeal origin of the minimal DsrABCMK(N) protein set, having as primordial function sulfite reduction. The acquisition of additional Dsr proteins (DsrJOPT) increased the Dsr pathway complexity. Archaeoglobus would originally possess the archaeal-type Dsr pathway and the archaeal DsrAB proteins were replaced with the bacterial reductive-type version, possibly at the same time as the acquisition of the QmoABC and DsrD proteins. Further inventions of two Qmo complex types, which are more spread than previously thought, allowed microorganisms to use sulfate as electron acceptor. The ability to use the Dsr pathway for sulfur oxidation evolved at least twice, with Chlorobi and Proteobacteria being extant descendants of these two independent adaptations.publishersversioninpres

Identification of the sirohaem biosynthesis pathway in Staphylococcus aureus

Sirohaem is a modified tetrapyrrole and a key prosthetic group of several enzymes involved in nitrogen and sulfur metabolisms. This work shows that Staphylococcus aureus produces sirohaem through a pathway formed by three independent enzymes. Of the two putative sirohaem synthases encoded in the S. aureus genome and annotated as cysG, one is herein shown to be a uroporphyrinogen III methyltransferase that converts uroporphyrinogen III to precorrin-2, and was renamed as UroM. The second cysG gene encodes a precorrin-2 dehydrogenase that converts precorrin-2 to sirohydrochlorin, and was designated as P2D. The last step was found to be performed by the gene nirR that, in fact, codes for a protein with sirohydrochlorin ferrochelatase activity, labelled as ShfC. Additionally, site-directed mutagenesis studies of S. aureus ShfC revealed that residues H22 and H87, which are predicted by homology modelling to be located at the active site, control the ferrochelatase activity. Within bacteria, sirohaem synthesis may occur via one, two or three enzymes, and we propose to name the correspondent pathways as Types 1, 2 and 3, respectively. A phylogenetic analysis revealed that Type 1 is the most used pathway in Gammaproteobacteria and Streptomycetales, Type 2 predominates in Fibrobacteres and Vibrionales, and Type 3 predominates in Firmicutes of the Bacillales order. Altogether, we concluded that the current distribution of sirohaem pathways within bacteria, which changes at the genus or species level and within taxa, seems to be the result of evolutionary multiple fusion/fission events.preprintpublishe

Lipid biosignature of breast cancer tissues by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Purpose One of the hallmarks of cancer cells is the demand of supply for the synthesis of new membranes involved in cell proliferation and lipids have an important role in cellular structure, signaling pathways and progression of cancer. In this sense, lipid studies have become an essential tool allowing the establishment of signatures associated with breast cancer (BC). In this regard, some metabolic processes including proteins, nucleic acids and lipid synthesis are enhanced as part of cancer-associated metabolic reprogramming, as a requirement for cell growth and proliferation. Methods Pairwise samples of breast active carcinoma (BAC) and breast cancer-free tissues were collected from n=28 patients and analyzed by MALDI-TOF MS. Results Major lipid species are identifed in the MALDI-TOF mass spectra, with certain phosphatidylinositols (PIs) detect able only in BAC. Statistical analysis revealed signifcant diferences (p<0.05) between ratios lysophosphatidylcholine (LPC) 16:0/phosphatidylcholine (PC) 16:0_18:2 between AC and CF groups as well as for BC stages II and III. The ratio PC 16:0_18:2/PC16:0_18:1 was statistically diferent between AC and CF groups. The one-way ANOVA revealed that there are no statistical diferences among BC stages (I, II and III) within AC group. Comparing BC stages, the signifcance impact increased (p<0.05) with stage. Conclusion The obtained data revealed MALDI-TOF MS as a powerful tool to explore lipid signatures and the enzyme activity associated with BC and possibly establish novel disease markers.info:eu-repo/semantics/publishedVersio

Plastid origin: who, when and why?

The origin of plastids is best explained by endosymbiotic theory, which dates back to the early 1900s. Three lines of evidence based on protein import machineries and molecular phylogenies of eukaryote (host) and cyanobacterial (endosymbiont) genes point to a single origin of primary plastids, a unique and important event that successfully transferred two photosystems and oxygenic photosynthesis from prokaryotes to eukaryotes. The nature of the cyanobacterial lineage from which plastids originated has been a topic of investigation. Recent studies have focused on the branching position of the plastid lineage in the phylogeny based on cyanobacterial core genes, that is, genes shared by all cyanobacteria and plastids. These studies have delivered conflicting results, however. In addition, the core genes represent only a very small portion of cyanobacterial genomes and may not be a good proxy for the rest of the ancestral plastid genome. Information in plant nuclear genomes, where most genes that entered the eukaryotic lineage through acquisition from the plastid ancestor reside, suggests that heterocyst-forming cyanobacteria in Stanier’s sections IV and V are most similar to the plastid ancestor in terms of gene complement and sequence conservation, which is in agreement with models suggesting an important role of nitrogen fixation in symbioses involving cyanobacteria. Plastid origin is an ancient event that involved a prokaryotic symbiont and a eukaryotic host, organisms with different histories and genome evolutionary processes. The different modes of genome evolution in prokaryotes and eukaryotes bear upon our interpretations of plastid phylogeny

Oxygen Reductases in Alphaproteobacterial Genomes: Physiological Evolution From Low to High Oxygen Environments

Oxygen reducing terminal oxidases differ with respect to their subunit composition, heme groups, operon structure, and affinity for O2. Six families of terminal oxidases are currently recognized, all of which occur in alphaproteobacterial genomes, two of which are also present in mitochondria. Many alphaproteobacteria encode several different terminal oxidases, likely reflecting ecological versatility with respect to oxygen levels. Terminal oxidase evolution likely started with the advent of O2 roughly 2.4 billion years ago and terminal oxidases diversified in the Proterozoic, during which oxygen levels remained low, around the Pasteur point (ca. 2 μM O2). Among the alphaproteobacterial genomes surveyed, those from members of the Rhodospirillaceae reveal the greatest diversity in oxygen reductases. Some harbor all six terminal oxidase types, in addition to many soluble enzymes typical of anaerobic fermentations in mitochondria and hydrogenosomes of eukaryotes. Recent data have it that O2 levels increased to current values (21% v/v or ca. 250 μM) only about 430 million years ago. Ecological adaptation brought forth different lineages of alphaproteobacteria and different lineages of eukaryotes that have undergone evolutionary specialization to high oxygen, low oxygen, and anaerobic habitats. Some have remained facultative anaerobes that are able to generate ATP with or without the help of oxygen and represent physiological links to the ancient proteobacterial lineage at the origin of mitochondria and eukaryotes. Our analysis reveals that the genomes of alphaproteobacteria appear to retain signatures of ancient transitions in aerobic metabolism, findings that are relevant to mitochondrial evolution in eukaryotes as well

Rodent models of Parkinson's disease: beyond the motor symptomatology

Parkinson's disease (PD) is classically characterized by motor symptoms; however, non-motor symptoms (NMS) are increasingly recognized as relevant in disease-state, given the associated alterations in mood (depression and anxiety) and cognition. Here, particularly in regards to NMS, we aimed to compare the motor, emotional and cognitive behavior of three animal models of PD that trigger dopaminergic (DAergic) degeneration on both brain hemispheres: (i) the 6-hydroxydopamine (6-OHDA, 8 or 6 µg) lesion model; (ii) the paraquat (PQ) induced model, and (iii) a genetic model based on a-synuclein overexpression (a-syn). 6-OHDA and a-syn vector were injected bilaterally in the substantia nigra pars compacta (SNpc) of adult male Wistar rats; as for PQ delivery, micro-osmotic pumps were implanted in the interscapular region. Motor deficits were observed in all models, with histological analysis of tyrosine hydroxylase positive cells in the SNpc revealing a significant loss of DAergic neurons in all animal models. In addition, the a-syn animal model also presented a reduction in exploratory activity, and the 6-OHDA and PQ animals displayed a significant increase in both depressive- and anxiety-like behavior. Interestingly, cognitive impairment (working memory) was only observed in the 6-OHDA model. Overall, these PD models are suitable for mimicking the motor symptoms associated to PD, with each encompassing other relevant NMS components of the disorder that may prove beneficial for further studies in PD.We would like to acknowledge the funds attributed by the Portuguese Foundation for Science and Technology (FCT), the PhD scholarships to E L. Campos (SFRH/BD/47311/2008) and M. M. Carvalho (SFRH/BD/51061/2010) and the Post-Doctoral fellowship to A. C. Cristovao (SFRH/BPD/69643/2010), and to Fundacao Calouste de Gulbenkian-Programme to Support Cutting Edge Research in Life Sciences and ICVS for funding this work. We want to further acknowledge Joao Cerqueira and Nadine Correia Santos for their contribution to this work

AlloRep: A Repository of Sequence, Structural and Mutagenesis Data for the LacI/GalR Transcription Regulators

Protein families evolve functional variation by accumulating point mutations at functionally important amino acid positions. Homologs in the LacI/GalR family of transcription regulators have evolved to bind diverse DNA sequences and allosteric regulatory molecules. In addition to playing key roles in bacterial metabolism, these proteins have been widely used as a model family for benchmarking structural and functional prediction algorithms. We have collected manually curated sequence alignments for >ﾠ3000 sequences, in vivo phenotypic and biochemical data for >ﾠ5750 LacI/GalR mutational variants, and noncovalent residue contact networks for 65 LacI/GalR homolog structures. Using this rich data resource, we compared the noncovalent residue contact networks of the LacI/GalR subfamilies to design and experimentally validate an allosteric mutant of a synthetic LacI/GalR repressor for use in biotechnology. The AlloRep database (freely available at www.AlloRep.org) is a key resource for future evolutionary studies of LacI/GalR homologs and for benchmarking computational predictions of functional change

Behavioral characterization of the 6-hydroxidopamine model of Parkinson's disease and pharmacological rescuing of non-motor deficits

BACKGROUND: Parkinson's disease (PD) is a chronic neurodegenerative condition that is characterized by motor symptoms as a result of dopaminergic degeneration, particularly in the mesostriatal pathway. However, in recent years, a greater number of clinical studies have focused on the emergence of non-motor symptoms in PD patients, as a consequence of damage on the mesolimbic and mesocortical dopaminergic networks, and on their significant impact on the quality of life of PD patients. Herein, we performed a thorough behavioral analysis including motor, emotional and cognitive dimensions, of the unilateral medial forebrain bundle (MFB) 6-hydroxidopamine (6-OHDA)-lesioned model of PD, and further addressed the impact of pharmacological interventions with levodopa and antidepressants on mood dimensions. RESULTS: Based on apomorphine-induced turning behaviour and degree of dopaminergic degeneration, animals submitted to MFB lesions were subdivided in complete and incomplete lesion groups. Importantly, this division also translated into a different severity of motor and exploratory impairments and depressive-like symptoms; in contrast, no deficits in anxiety-like and cognitive behaviors were found in MFB-lesioned animals. Subsequently, we found that the exploratory and the anhedonic behavioural alterations of MFB-lesioned rats can be partially improved with the administration of both levodopa or the antidepressant bupropion, but not paroxetine. CONCLUSIONS: Our results suggest that this model is a relevant tool to study the pathophysiology of motor and non-motor symptoms of PD. In addition, the present data shows that pharmacological interventions modulating dopaminergic transmission are also relevant to revert the non-motor behavioral deficits found in the disease.We would like to acknowledge the funds attributed by Fundacao Calouste de Gulbenkian to A.J. Salgado under the scope of the The Gulbenkian Program to Support Research in the Life Sciences, and Portuguese Foundation for Science and Technology: Ciencia 2007 Program to A.J. Salgado; the PhD scholarships to M. M. Carvalho (SFRH/BD/51061/2010) and F. L. Campos (SFRH/BD/47311/2008), and the Post-Doctoral Fellowship to A.J. Rodrigues (SFRH/BPD/33611/2009) We want to further acknowledge Carina Cunha, Fabio Teixeira, Joao Bessa and Joao Cerqueira for their contribution to this work

Neudesin is involved in anxiety behavior: structural and neurochemical correlates

Neudesin (also known as neuron derived neurotrophic factor, Nenf) is a scarcely studied putative non-canonical neurotrophic factor. In order to understand its function in the brain, we performed an extensive behavioral characterization (motor, emotional, and cognitive dimensions) of neudesin-null mice. The absence of neudesin leads to an anxious-like behavior as assessed in the elevated plus maze (EPM), light/dark box (LDB) and novelty suppressed feeding (NSF) tests, but not in the acoustic startle (AS) test. This anxious phenotype is associated with reduced dopaminergic input and impoverished dendritic arborizations in the dentate gyrus granule neurons of the ventral hippocampus. Interestingly, shorter dendrites are also observed in the bed nucleus of the stria terminalis (BNST) of neudesin-null mice. These findings lead us to suggest that neudesin is a novel relevant player in the maintenance of the anxiety circuitry.This work is supported by a grant from FCT (PTDC/SAU-OSM/104475/2008) under POCTI-COMPETE funds. Ashley Novais, Ana Catarina Ferreira, Ana David-Pereira and Filipa L. Campos are recipients of doctoral fellowships and Fernanda Marques is a recipient of postdoctoral fellowship from Fundacao para a Ciencia e Tecnologia (FCT), Portugal. We acknowledge Merck Serono for providing the neudesin-null mouse strain. We are thankful to Despina Papasava and Vasileios Kafetzopoulos for the assistance given in the HPLC analysis of neurotransmitters

Energy at Origins: Favorable Thermodynamics of Biosynthetic Reactions in the Last Universal Common Ancestor (LUCA)

Though all theories for the origin of life require a source of energy to promote primordial chemical reactions, the nature of energy that drove the emergence of metabolism at origins is still debated. We reasoned that evidence for the nature of energy at origins should be preserved in the biochemical reactions of life itself, whereby changes in free energy, ΔG, which determine whether a reaction can go forward or not, should help specify the source. By calculating values of ΔG across the conserved and universal core of 402 individual reactions that synthesize amino acids, nucleotides and cofactors from H2, CO2, NH3, H2S and phosphate in modern cells, we find that 95-97% of these reactions are exergonic (ΔG ≤ 0 kJ⋅mol-1) at pH 7-10 and 80-100°C under nonequilibrium conditions with H2 replacing biochemical reductants. While 23% of the core's reactions involve ATP hydrolysis, 77% are ATP-independent, thermodynamically driven by ΔG of reactions involving carbon bonds. We identified 174 reactions that are exergonic by -20 to -300 kJ⋅mol-1 at pH 9 and 80°C and that fall into ten reaction types: six pterin dependent alkyl or acyl transfers, ten S-adenosylmethionine dependent alkyl transfers, four acyl phosphate hydrolyses, 14 thioester hydrolyses, 30 decarboxylations, 35 ring closure reactions, 31 aromatic ring formations, and 44 carbon reductions by reduced nicotinamide, flavins, ferredoxin, or formate. The 402 reactions of the biosynthetic core trace to the last universal common ancestor (LUCA), and reveal that synthesis of LUCA's chemical constituents required no external energy inputs such as electric discharge, UV-light or phosphide minerals. The biosynthetic reactions of LUCA uncover a natural thermodynamic tendency of metabolism to unfold from energy released by reactions of H2, CO2, NH3, H2S, and phosphate