DsrMKJOP is the terminal reductase complex in anaerobic sulfate respiration.

Microbial dissimilatory sulfate reduction (DSR) is a key process in the Earth biogeochemical sulfur cycle. In spite of its importance to the sulfur and carbon cycles, industrial processes, and human health, it is still not clear how reduction of sulfate to sulfide is coupled to energy conservation. A central step in the pathway is the reduction of sulfite by the DsrAB dissimilatory sulfite reductase, which leads to the production of a DsrC-trisulfide. A membrane-bound complex, DsrMKJOP, is present in most organisms that have DsrAB and DsrC, and its involvement in energy conservation has been inferred from sequence analysis, but its precise function was so far not determined. Here, we present studies revealing that the DsrMKJOP complex of the sulfate reducer Archaeoglobus fulgidus works as a menadiol:DsrC-trisulfide oxidoreductase. Our results reveal a close interaction between the DsrC-trisulfide and the DsrMKJOP complex and show that electrons from the quinone pool reduce consecutively the DsrM hemes b, the DsrK noncubane [4Fe-4S]3+/2+ catalytic center, and finally the DsrC-trisulfide with concomitant release of sulfide. These results clarify the role of this widespread respiratory membrane complex and support the suggestion that DsrMKJOP contributes to energy conservation upon reduction of the DsrC-trisulfide in the last step of DSR.

The DsrD functional marker protein is an allosteric activator of the DsrAB dissimilatory sulfite reductase.

Dissimilatory sulfur metabolism was recently shown to be much more widespread among bacteria and archaea than previously believed. One of the key pathways involved is the dsr pathway that is responsible for sulfite reduction in sulfate-, sulfur-, thiosulfate-, and sulfite-reducing organisms, sulfur disproportionators and organosulfonate degraders, or for the production of sulfite in many photo- and chemotrophic sulfur-oxidizing prokaryotes. The key enzyme is DsrAB, the dissimilatory sulfite reductase, but a range of other Dsr proteins is involved, with different gene sets being present in organisms with a reductive or oxidative metabolism. The dsrD gene codes for a small protein of unknown function and has been widely used as a functional marker for reductive or disproportionating sulfur metabolism, although in some cases this has been disputed. Here, we present in vivo and in vitro studies showing that DsrD is a physiological partner of DsrAB and acts as an activator of its sulfite reduction activity. DsrD is expressed in respiratory but not in fermentative conditions and a ΔdsrD deletion strain could be obtained, indicating that its function is not essential. This strain grew less efficiently during sulfate and sulfite reduction. Organisms with the earliest forms of dsrAB lack the dsrD gene, revealing that its activating role arose later in evolution relative to dsrAB.

Dynamics of the sucrose metabolism and related gene expression in tomato fruits under water deficit.

The impact of water deficit on sucrose metabolism in sink organs like the fruit remains poorly known despite the need to improve fruit crops resilience to drought in the face of climate change. The present study investigated the effects of water deficit on sucrose metabolism and related gene expression in tomato fruits, aiming to identify candidate genes for improving fruit quality upon low water availability. Tomato plants were subjected to irrigated control and water deficit (-60% water supply compared to control) treatments, which were applied from the first fruit set to first fruit maturity stages. The results have shown that water deficit significantly reduced fruit dry biomass and number, among other plant physiological and growth variables, but substantially increased the total soluble solids content. The determination of soluble sugars on the basis of fruit dry weight revealed an active accumulation of sucrose and concomitant reduction in glucose and fructose levels in response to water deficit. The complete repertoire of genes encoding sucrose synthase (SUSY1-7), sucrose-phosphate synthase (SPS1-4), and cytosolic (CIN1-8), vacuolar (VIN1-2) and cell wall invertases (WIN1-4) was identified and characterized, of which SlSUSY4, SlSPS1, SlCIN3, SlVIN2, and SlCWIN2 were shown to be positively regulated by water deficit. Collectively, these results show that water deficit regulates positively the expression of certain genes from different gene families related to sucrose metabolism in fruits, favoring the active accumulation of sucrose in this organ under water-limiting conditions. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01288-7.

Improving the Biodesulfurization of Crude Oil and Derivatives: A QM/MM Investigation of the Catalytic Mechanism of NADH-FMN Oxidoreductase (DszD).

The development of biocatalytic desulfurization strategies of petroleum and its derivatives could result in more economic alternatives than the widely used chemical desulfurization. The organism Rhodococcus erythropolis IGTS8 has been shown to metabolize organic sulfur compounds through a mechanism known as 4S pathway, which involves four enzymes (DszA, DszB, DszC, and DszD) and has been explored in biodesulfurization. Here we have applied QM/MM methods to study the catalytic mechanism of the enzyme DszD, a NADH-FMN oxidoreductase that occupies a central place on the 4S pathway by catalyzing the formation of the FMNH2 that is used by the two monooxynases in the cycle: DszA and DszC. In addition, to clarify the catalytic mechanism of this enzyme, this study analyzed in detail the role played by the active site Thr residue and of Asn and Ala enzyme mutants. The results help to explain previous experimental evidence and suggest new strategies for improving biodesulfurization through an increase in the activity of DszD.

Therapeutic futility in cancer patients at the time of palliative care transition: An analysis with a modified version of the Medication Appropriateness Index.

BACKGROUND: Palliative Care professionals are often confronted with therapeutic futility, consisting in inappropriate strategies that do not add any advantage to the patient and may actually increase adverse events. Scientific literature concerning this issue is lacking. This article is one of the first to study therapeutic futility specifically at the time of transition to the palliative care setting. AIM: To study the phenomenon of pharmacologic therapeutic futility at the time of transition of a cancer patient to palliative care. DESIGN: The pharmacological prescriptions at the time of the first appointment at an oncological palliative care unit during a time period of 2 months were prospectively collected and characterized using the Medication Appropriateness Index. PARTICIPANTS: The sample comprised 71 patients with a mean age of 68.2 years. RESULTS: The most common pharmacological groups were analgesics (n = 121; 19.2%), psychoactive drugs (n = 89; 14.1%), and antihypertensives (n = 51; 8.1%). A total of 61 patients (85.9%) consumed 5 drugs or more at the time of the first appointment. The mean number of daily medications decreased significantly after the palliative care team intervention, from 7.15 to 5.73 (p < 0.05). The principal causes of inappropriateness were absence of indication for the drug (23.0% "inappropriate"), the drugs' adverse interactions (11.1%), and inadequate dosage (9.9%). After the first consultation in the palliative care setting, 28.2% of the drugs were suspended. CONCLUSION: This article tried to evaluate the main causes of therapeutic futility at the palliative care transition. The principal causes of inappropriateness were absence of clinical indication, clinically significant drug-disease/comorbidity interactions, and incorrect dosage/posology.

Identification of DEMETER-like DNA demethylase gene family in citrus and their role in drought stress-adaptive responses.

DEMETER-Like DNA demethylases (DMLs) are epigenetic regulators of many developmental and biological processes in plants. No comprehensive information about the DML gene family in citrus is available to date. Here, a total of three DML genes in the genomes of Citrus sinensis (named CsDML1-3) and C. clementina (named CcDML1-3) were identified and analyzed. They encode hydrophilic and relatively large proteins, with prediction of nuclear localization, containing the conserved domains and motifs typical of plant DMLs. Protein interaction network analysis suggested that they interact primarily with proteins related to the maintenance of DNA methylation and remodeling of chromatin. Analysis of their promoter regions led to the identification of several cis-acting regulatory elements involved in stress response, including drought, heat and cold stresses. The presence of several miRNA targets and potential phosphorylation sites suggest that their expression is also regulated at post-transcriptional and post-translational levels. RNA-Seq data and quantitative real-time PCR analysis showed a low and drought-regulated gene expression of the citrus DMLs in different plant tissues. CsDML1 and CsDML3 were also differentially regulated by deficit irrigation in fruits at different developmental stages, with a positive and significant correlation found between CsDML1 and PHYTOENE SYNTHASE (PSY) and between CsDML3 and ATP CITRATE LYASEs (ACLs) and ZETA-CAROTENE DESATURASE (ZDS) gene expression. These results indicate that the citrus DMLs are potentially functional enzymes involved in developmental processes and drought stress-adaptive responses, providing a useful reference for further investigation of their functions and applications on the citrus improvement.

Histone deacetylases 1 and 2 control the progression of neural precursors to neurons during brain development.

The molecular mechanism by which neural progenitor cells commit to a specified lineage of the central nervous system remains unknown. We show that HDAC1 and HDAC2 redundantly control neuronal development and are required for neuronal specification. Mice lacking HDAC1 or HDAC2 in neuronal precursors show no overt histoarchitectural phenotypes, whereas deletion of both HDAC1 and HDAC2 in developing neurons results in severe hippocampal abnormalities, absence of cerebellar foliation, disorganization of cortical neurons, and lethality by postnatal day 7. These abnormalities in brain formation can be attributed to a failure of neuronal precursors to differentiate into mature neurons and to excessive cell death. These results reveal redundant and essential roles for HDAC1 and HDAC2 in the progression of neuronal precursors to mature neurons in vivo.

MEF2C, a transcription factor that facilitates learning and memory by negative regulation of synapse numbers and function.

Learning and memory depend on the activity-dependent structural plasticity of synapses and changes in neuronal gene expression. We show that deletion of the MEF2C transcription factor in the CNS of mice impairs hippocampal-dependent learning and memory. Unexpectedly, these behavioral changes were accompanied by a marked increase in the number of excitatory synapses and potentiation of basal and evoked synaptic transmission. Conversely, neuronal expression of a superactivating form of MEF2C results in a reduction of excitatory postsynaptic sites without affecting learning and memory performance. We conclude that MEF2C limits excessive synapse formation during activity-dependent refinement of synaptic connectivity and thus facilitates hippocampal-dependent learning and memory.

Redox loops in anaerobic respiration - The role of the widespread NrfD protein family and associated dimeric redox module.

In prokaryotes, the proton or sodium motive force required for ATP synthesis is produced by respiratory complexes that present an ion-pumping mechanism or are involved in redox loops performed by membrane proteins that usually have substrate and quinone-binding sites on opposite sides of the membrane. Some respiratory complexes include a dimeric redox module composed of a quinone-interacting membrane protein of the NrfD family and an iron­sulfur protein of the NrfC family. The QrcABCD complex of sulfate reducers, which includes the QrcCD module homologous to NrfCD, was recently shown to perform electrogenic quinone reduction providing the first conclusive evidence for energy conservation among this family. Similar redox modules are present in multiple respiratory complexes, which can be associated with electroneutral, energy-driven or electrogenic reactions. This work discusses the presence of the NrfCD/PsrBC dimeric redox module in different bioenergetics contexts and its role in prokaryotic energy conservation mechanisms.

The barnacle Chthamalus bisinuatus is the only sessile invertebrate colonizing oil patches on beachrocks one year after a massive oil spill on the Northeastern Brazilian coast.

A large-scale oil spill has reached over 3000 km of the NE Brazilian coast since August 2019. The cause and origin of this spill remain mysterious, and the impacts on coastal ecosystems have not been clearly understood so far. Despite the efforts to remove the oil (mainly from local communities), oil stains are still present in beaches, mangroves, and beachrocks. In this short report, we describe the occurrence of the barnacle Chthamalus bisinuatus Pilsbry, 1916 colonizing oil spill stains on intertidal surfaces of beachrocks one year after the first oil records. We quickly assessed oil stains across three different reefs located at the Conde municipality, Bahia (NE Brazil), where the species was identified and its density on oil stains calculated. The occurrence of barnacles in oil stains was restricted to zones in the wake of the reefs. Their densities varied from 0 to 238 ind./dm2, with an average of 34 ± 68 ind./dm2. If we account for dead individuals (empty barnacle plates), they correspond to 25.9% of the sampled population. The presence of oil possibly affected barnacle survival rates but did not seem to prevent barnacle individuals from reaching adult sizes. We also found individuals of the snail Echinolittorina lineolata (d'Orbigny, 1840) crawling on these barnacles, indicating that the barnacle assemblages on oil stains are stable enough to provide refuge for these snails. It is not clear if the presence of barnacles on oil reflects the resistance of these crustaceans to the oil toxicity or is just a result of a low substrate selectivity by the cypris larvae.

Polycyclic aromatic hydrocarbons in sediments and shellfish from Todos os Santos bay, Brazil.

The present study evaluated the occurrence of 24 Polycyclic Aromatic Hydrocarbons (PAHs) in sediments and shellfish (Anomalocardia flexuosa, Crassostrea rhizophorae, and Mytella guyanensis) of Todos os Santos bay (BTS, Brazil). Total PAHs levels ranged from 89 to 921 ng g-1 dry weight (d.w.) in sediments, and from 66 to 505 ng g-1 d.w. in shellfish, signalizing that BTS was moderately contaminated by PAHs, mostly from pyrogenic activities. The bioaccumulation factor (BAF) of total PAHs ranged from 0.20 to 2.9 and did not show a clear trend among the studied species. BAFs of high molecular weight compounds were higher for A. flexuosa (specie found buried in fine sediment), while those of low molecular weight compounds were higher for C. rhizophorae (specie found in the roots of mangrove trees). High concentrations of PAHs, especially benzo[a]pyrene and dibenzo[a,h]anthracene, suggest that contamination compromises shellfish quality and raise concern about seafood consumption safety.

Persistent organic pollutants (POPs) and personal care products (PCPs) in the surface sediments of a large tropical bay (Todos os Santos Bay, Brazil).

The occurrence and spatial distribution of persistent organic pollutants (POPs) and personal care products (PCPs) were investigated in surface sediments of Todos os Santos Bay. Samples were Soxhlet-extracted and analyzed by gas chromatography coupled with tandem mass spectrometry. Quantification limits (QL) ranged from 0.0025 ng g-1 for POPs to 0.25 ng g-1 for PCPs. Of the POPs studied, only PCBs and DDTs were detectable, with concentrations ranging from

DNA binding-dependent and -independent functions of the Hand2 transcription factor during mouse embryogenesis.

The basic helix-loop-helix (bHLH) transcription factor Hand2 is required for growth and development of the heart, branchial arches and limb buds. To determine whether DNA binding is required for Hand2 to regulate the growth and development of these different embryonic tissues, we generated mutant mice in which the Hand2 locus was modified by a mutation (referred to as Hand2(EDE)) that abolished the DNA-binding activity of Hand2, leaving the remainder of the protein intact. In contrast to Hand2 null embryos, which display right ventricular hypoplasia and vascular abnormalities, causing severe growth retardation by E9.5 and death by E10.5, early development of the heart appeared remarkably normal in homozygous Hand2(EDE) mutant embryos. These mutant embryos also lacked the early defects in growth of the branchial arches seen in Hand2 null embryos and survived up to 2 to 3 days longer than did Hand2 null embryos. However, Hand2(EDE) mutant embryos exhibited growth defects in the limb buds similar to those of Hand2 null embryos. These findings suggest that Hand2 regulates tissue growth and development in vivo through DNA binding-dependent and -independent mechanisms.

Hand transcription factors cooperatively regulate development of the distal midline mesenchyme.

Hand proteins are evolutionally conserved basic helix-loop-helix (bHLH) transcription factors implicated in development of neural crest-derived tissues, heart and limb. Hand1 is expressed in the distal (ventral) zone of the branchial arches, whereas the Hand2 expression domain extends ventrolaterally to occupy two-thirds of the mandibular arch. To circumvent the early embryonic lethality of Hand1 or Hand2-null embryos and to examine their roles in neural crest development, we generated mice with neural crest-specific deletion of Hand1 and various combinations of mutant alleles of Hand2. Ablation of Hand1 alone in neural crest cells did not affect embryonic development, however, further removing one Hand2 allele or deleting the ventrolateral branchial arch expression of Hand2 led to a novel phenotype presumably due to impaired growth of the distal midline mesenchyme. Although we failed to detect changes in proliferation or apoptosis between the distal mandibular arch of wild-type and Hand1/Hand2 compound mutants at embryonic day (E)10.5, dysregulation of Pax9, Msx2 and Prx2 was observed in the distal mesenchyme at E12.5. In addition, the inter-dental mesenchyme and distal symphysis of Meckel's cartilage became hypoplastic, resulting in the formation of a single fused lower incisor within the hypoplastic fused mandible. These findings demonstrate the importance of Hand transcription factors in the transcriptional circuitry of craniofacial and tooth development.

Coactivation of MEF2 by the SAP domain proteins myocardin and MASTR.

Myocardin is a cardiac- and smooth muscle-specific SAP domain transcription factor that functions as a coactivator for serum response factor (SRF), which controls genes involved in muscle differentiation and cell proliferation. The DNA binding domain of SRF, which interacts with myocardin, shares homology with the MEF2 transcription factor, which also controls muscle and growth-associated genes. Here we show that alternative splicing produces a cardiac-enriched isoform of myocardin containing a unique peptide sequence that confers the ability to interact with and stimulate the transcriptional activity of MEF2. This MEF2 binding motif is also contained in a previously unknown SAP domain transcription factor, referred to as MASTR, which functions as a MEF2 coactivator. This unique protein-protein interaction motif expands the regulatory potential of myocardin, and its presence in MASTR reveals a new mechanism for the control of MEF2 activity.

The Hand1 and Hand2 transcription factors regulate expansion of the embryonic cardiac ventricles in a gene dosage-dependent manner.

The basic helix-loop-helix transcription factors Hand1 and Hand2 display dynamic and spatially restricted expression patterns in the developing heart. Mice that lack Hand2 die at embryonic day 10.5 from right ventricular hypoplasia and vascular defects, whereas mice that lack Hand1 die at embryonic day 8.5 from placental and extra-embryonic abnormalities that preclude analysis of its potential role in later stages of heart development. To determine the cardiac functions of Hand1, we generated mice harboring a conditional Hand1-null allele and excised the gene by cardiac-specific expression of Cre recombinase. Embryos homozygous for the cardiac Hand1 gene deletion displayed defects in the left ventricle and endocardial cushions, and exhibited dysregulated ventricular gene expression. However, these embryos survived until the perinatal period when they died from a spectrum of cardiac abnormalities. Creation of Hand1/2 double mutant mice revealed gene dose-sensitive functions of Hand transcription factors in the control of cardiac morphogenesis and ventricular gene expression. These findings demonstrate that Hand factors play pivotal and partially redundant roles in cardiac morphogenesis, cardiomyocyte differentiation and cardiac-specific transcription.

Histone deacetylase 4 controls chondrocyte hypertrophy during skeletogenesis.

Histone deacetylases (HDACs) modulate cell growth and differentiation by governing chromatin structure and repressing the activity of specific transcription factors. We showed previously that HDAC9 acts as a negative regulator of cardiomyocyte hypertrophy and skeletal muscle differentiation. Here we report that HDAC4, which is expressed in prehypertrophic chondrocytes, regulates chondrocyte hypertrophy and endochondral bone formation by interacting with and inhibiting the activity of Runx2, a transcription factor necessary for chondrocyte hypertrophy. HDAC4-null mice display premature ossification of developing bones due to ectopic and early onset chondrocyte hypertrophy, mimicking the phenotype that results from constitutive Runx2 expression in chondrocytes. Conversely, overexpression of HDAC4 in proliferating chondrocytes in vivo inhibits chondrocyte hypertrophy and differentiation, mimicking a Runx2 loss-of-function phenotype. These results establish HDAC4 as a central regulator of chondrocyte hypertrophy and skeletogenesis and suggest general roles for class II HDACs in the control of cellular hypertrophy.