bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of insect and human cytochrome b561 proteins: Insights into candidate ferric reductases in insects
Authors: Holst Jessica D. , Murphy Laura G. , Gorman Maureen J. , Ragan Emily J. 
Published: September 2023

AbstractCytochrome b561 (cytb561) proteins comprise a family of transmembrane oxidoreductases that transfer single electrons across a membrane. Most eukaryotic species, including insects, possess multiple cytb561 homologs. To learn more about this protein family in insects, we carried out a bioinformatics-based investigation of cytb561 family members from nine species representing eight insect orders. We performed a phylogenetic analysis to classify insect cytb561 orthologous groups. We then conducted sequence analyses and analyzed protein models to predict structural elements that may impact the biological functions and localization of these proteins, with a focus on possible ferric reductase activity. Our study revealed three orthologous groups, designated CG1275, Nemy, and CG8399, and a fourth group of less-conserved genes. We found that CG1275 and Nemy proteins are similar to a human ferric reductase, duodenal cytochrome b561 (Dcytb), and have many conserved amino acid residues that function in substrate binding in Dcytb. Notably, CG1275 and Nemy proteins contain a conserved histidine and other residues that play a role in ferric ion reduction by Dcytb. Nemy proteins were distinguished by a novel cysteine-rich cytoplasmic loop sequence. CG8399 orthologs are similar to a putative ferric reductase in humans, stromal cell-derived receptor 2. Like other members of the CYBDOM class of cytb561 proteins, these proteins contain reeler, DOMON, and cytb561 domains.Drosophila melanogasterCG8399 is the only insect cytb561 with known ferric reductase activity. Our investigation of the DOMON domain in CG8399 proteins revealed a probable heme-binding site and a possible site for ferric reduction. The fourth clade includes a group of proteins with a conserved “KXXXXKXH” non-cytoplasmic loop motif that may be a substrate binding site and is present in a potential ferric reductase, human tumor suppressor cytochrome b561. This study provides a foundation for future investigations of the biological functions of cytb561 genes in insects.
A rapid and dynamic role for FMRP in the plasticity of adult neurons
Authors: Gundermann Daniel G. , Lymer Seana , Blau Justin 
Published: September 2023

AbstractFragile X syndrome (FXS) is a neuro-developmental disorder caused by silencingFmr1, which encodes the RNA-binding protein FMRP. AlthoughFmr1is expressed in adult neurons, it has been challenging to separate acute from chronic effects of loss ofFmr1in models of FXS. We have used the precision ofDrosophilagenetics to test ifFmr1acutely affects adult neuronal plasticityin vivo, focusing on the s-LNv circadian pacemaker neurons that show 24 hour rhythms in structural plasticity. We found that over-expressingFmr1for only 4 hours blocks the activity-dependent expansion of s-LNv projections without altering the circadian clock or activity- regulated gene expression. Conversely, acutely reducingFmr1expression prevented s-LNv projections from retracting. One FMRP target that we identified in s-LNvs issif, which encodes a Rac1 GEF. Our data indicate that FMRP normally reducessifmRNA translation at dusk to reduce Rac1 activity. Overall, our data reveal a previously unappreciated rapid and direct role for FMRP in acutely regulating neuronal plasticity in adult neurons, and underscore the importance of RNA-binding proteins in this process.
Phage libraries screening on P53 : yield improvement by zinc and a new parasites-integrating analysis and rationale
Authors: Ben Abid Sihem , Ketata Emna , Yacoubi-Hadj Amor Ines , Abdelmoula-Souissi Salma , Djemal Lamia , Koubaa Aida , Mokdad-Gargouri Raja , Gargouri Ali 
Published: September 2023

AbstractP53 is a transcription factor that controls a variety of genes, primarily involved in cell cycle and other processes related to cell survival and death. We have isolated peptides targeting P53 (protein and domains) using the “phage display” technique. Interestingly, adding ZnCl2 at 5-10 mM in panning solutions helped to recover more plaque-forming units at least at round one of the screening. Subtractive docking analyses were designed by using a pool of common redundant peptides known asparasites. This rationale helped us differentiate between possibly specific and non-specific bindings. We found notable differences in docking characteristics between different sets of peptides either related to different targets or related to zinc-conditions. The set of zinc-related peptides shows advantageous docking profiles: sharper binding for some positions and distinct exclusive bound residues, including the relevant R248 and R273. Zinc would have modulating/helping role in the targeting of protein P53 by phage displayed peptides in addition to an enhancement action on bacterial infection.
Disruption of Synaptic Endoplasmic Reticulum Luminal Protein Containment inDrosophila AtlastinMutants
Authors: Quiñones-Frías Mónica C. , Ocken Dina M. , Rodal Avital 
Published: September 2023

AbstractThe endoplasmic reticulum (ER) extends throughout neurons and regulates many neuronal functions, including neurite outgrowth, neurotransmission, and synaptic plasticity. Mutations in proteins that control ER shape are linked to the neurodegenerative disorder Hereditary Spastic Paraplegia (HSP), yet the ultrastructure and dynamics of neuronal ER remain largely unexplored, especially at presynaptic terminals. Using super-resolution and live imaging inD. melanogasterlarval motor neurons, we investigated ER structure at presynaptic terminals of wild-type animals and null mutants of the ER shaping protein and HSP-linked gene, Atlastin. Previous studies using an ER luminal marker reported diffuse localization atAtlastinmutant presynaptic terminals, which was attributed to ER fragmentation. However, using an ER membrane marker, we discovered thatAtlastinmutant ER forms robust networks with only mild defects in structural dynamics, indicating the primary defect is functional rather than architectural. We demonstrate thatAtlastinmutants progressively displace overexpressed luminal ER proteins to the cytosol during larval development, specifically at synapses, while these proteins remain correctly localized in cell bodies, axons, and muscles. This synaptic-specific displacement phenotype, previously unreported in non-neuronal cells, emphasizes the importance of studying neurons to understand HSP pathogenesis.
The role offruitlessin specifying courtship behaviors differs acrossDrosophilaspecies
Authors: Baker Christa A. , Guan Xiao-Juan , Choi Minseung , Murthy Mala 
Published: September 2023

AbstractSex-specific behaviors are critical for reproduction and species survival. The sex-specifically spliced transcription factorfruitless(fru) helps establish male courtship behaviors in invertebrates. Forcing male-specificfru(fruM) splicing inDrosophila melanogasterfemales produces male-typical behaviors, while disrupting female-specific behaviors. However, whetherfru’s joint role in specifying male and inhibiting female behaviors is conserved across species is unknown. We used CRISPR/Cas9 to force FruM expression in femaleD. virilis, a species in which males and females produce sex-specific songs. In contrast toD. melanogaster, in which onefruMallele is sufficient to generate male behaviors in females, two alleles are needed inD. virilisfemales.D. virilisfemales expressing FruM maintain the ability to sing female-typical song as well as lay eggs, whereasD. melanogasterFruM females cannot lay eggs. These results reveal important differences infrufunction between divergent species and underscore the importance of studying diverse behaviors and species for understanding the genetic basis of sex differences.
UK healthcare professionals’ attitudes towards the introduction of varicella vaccine into the routine childhood vaccination schedule and their preferences for delivery
Authors: Sherman Susan M. , Allerton-Price Charlotte , Lingley-Heath Nicola , Lai Jasmine , Bedford Helen 
Published: September 2023

ABSTRACTBackgroundVaricella (chickenpox) is a highly contagious disease caused by the varicella-zoster virus. Although typically a mild disease, varicella can cause complications leading to severe illness and even death. Safe and effective varicella vaccines are available. The Joint Committee on Vaccination and Immunisation is planning to review the evidence regarding the introduction of varicella vaccine into the UK’s routine childhood immunisation schedule.ObjectivesTo explore UK healthcare professionals’ (HCPs) knowledge and attitudes towards varicella vaccination, its introduction to the UK routine childhood immunisation schedule, and their preferences for how it should be delivered.DesignWe conducted an online cross-sectional survey exploring HCPs’ attitudes towards varicella, varicella vaccine, and their preferences for delivery of the vaccine between August and September 2022.Participants91 HCPs working in the UK (96.7% female, 3.3% male, mean age 48.7 years).ResultsGeneral vaccine attitudes in this group were very positive. Gaps in knowledge about varicella were revealed: 21.0% of respondents disagreed or were unsure that chickenpox can cause serious complications, while 41.8% were unsure or did not believe chickenpox was serious enough to vaccinate against. After receiving some basic information about chickenpox and the vaccine, almost half of the HCPs (47.3%) in our survey would prefer to administer the varicella vaccine combined with MMR.ConclusionsGiven the positive influence of HCPs on parents’ decisions to vaccinate their children, it is important to understand HCPs’ views regarding the introduction of varicella vaccine into the routine schedule. Our findings highlighted areas for training and HCPs’ preferences which will have implications for policy and practice should the vaccine be introduced.
Delayed localization of A-type lamins to the rupture sites in Hutchinson–Gilford progeria syndrome
Authors: Kono Yohei , Pack Chan-Gi , Ichikawa Takehiko , Komatsubara Arata , Adam Stephen A. , Miyazawa Keisuke , Rolas Loïc , Nourshargh Sussan , Medalia Ohad , Goldman Robert D. , Fukuma Takeshi , Kimura Hiroshi , Shimi Takeshi 
Published: September 2023

AbstractThe nuclear lamina (NL) lines the nuclear envelope (NE) to maintain nuclear structure in metazoan cells. The major NL components, the nuclear lamins contribute to the protection against NE rupture induced by mechanical stress. Lamin A (LA) and a short form of the splicing variant lamin C (LC) are diffused from the nucleoplasm to sites of NE rupture in immortalized mouse embryonic fibroblasts (MEFs). LA localization to the rupture sites is significantly slow and weak compared to LC because of its relatively small pool in the nucleoplasm, but the precise mechanism remains unknown. In this study, we induce NE rupture in wild-type and LA/C-knockout MEFs, and Hutchinson–Gilford Progeria syndrome (HGPS) knock-in MEFs that express progerin, a LA mutant lacking the second proteolytic cleavage site, by laser microirradiation and AFM indentation. The farnesylation at the CaaX motif of unprocessed LA and the inhibition of the second proteolytic cleavage decrease the nucleoplasmic pool and slow the localization to the rupture sites in a long-time window (60-70 min) after the induction of NE rupture. Our data could explain the defective repair of NE rupture in HGPS through the farnesylation at the CaaX motif of unprocessed progerin. In addition, unique segments in LA-specific tail region cooperate with each other to inhibit the rapid accumulation within a short-time window (3 min) that is also observed with LC.Significance StatementNuclear lamins are the major components of the nuclear lamina (NL) that lies the nuclear envelope (NE). Lamin A (LA) is slowly localized to sites of nuclear envelope (NE) rupture compared to lamin C (LC). This study reveals that the farnesylation at the CaaX motif of unprocessed LA and the inhibition of the second proteolytic cleavage decrease the nucleoplasmic pool and slow the localization to the rupture sites within a long-time window (60-70 min) after the induction of NE rupture, which could explain the defective repair of NE rupture in Hutchinson–Gilford Progeria syndrome (HGPS). Additionally, unique segments in LA-specific tail region are critical for inhibiting the rapid accumulation within a short-time window (3 min).
Regulation of an antibiotic resistance efflux pump by quorum sensing and a TetR-family repressor inChromobacterium subtsugae
Authors: Koirala Pratik , Doody Cassie , Blackwell Helen , Chandler Josephine R. 
Published: September 2023

AbstractThe soil bacteriumChromobacterium substugaeuses a single LuxI-R-type quorum-sensing system, CviI-R, to regulate genes in a cell density-dependent manner. CviI synthesizes the signalN-hexanoyl-homoserine lactone (C6-HSL) and CviR is a C6-HSL-responsive cytoplasmic transcription regulator. C6-HSL-bound CviR activates dozens of genes, for example thecdeAB-oprMcluster coding for an efflux pump conferring antibiotic resistance. ThecdeAB-oprMgenes are also regulated by an antibiotic-responsive transcription factor, CdeR, which represses expression of these genes. We are interested in understanding howC. subtsugaeintegrates different environmental cues to regulate antibiotic resistance. In this study, we sought to delineate the mechanism of regulation of thecdeAB-oprMgenes by CviR and CdeR. In recombinantE. coli,thecdeApromoter is activated by CviR and repressed by CdeR. We identify non-overlapping sequence elements in thecdeApromoter that are required for CviR activation and CdeR repression, respectively. We also examined the role of CdeR in modulatingcdeAactivation by C6-HSL inC. subtsugae. We show that CviR and CdeR can independently modulate transcription from thecdeApromoter inC. subtsugae, consistent with the conclusion that CviR and CdeR regulate thecdeAB-oprMgenes by interacting directly with different binding sites in thecdeApromoter. These results contribute to a molecular understanding of how thecdeAB-oprMgenes are regulated and provide new insight into howC. subtsugaeintegrates different environmental cues to regulate antibiotic resistance.ImportanceMany bacteria regulate antibiotic resistance in response to antibiotics and other cues from the environment. In many cases the regulatory mechanisms are best understood in the context of clinical isolates where mutations frequently emerge in resistance regulation pathways. However, an understanding of the role of antibiotic resistance regulators in integrating environmental information is less well understood. In the soil bacteriumChromobacterium subtsugae,an antibiotic-resistance gene cluster is regulated by population density and antibiotics through two different transcription factors; the quorum sensing signal receptor CviR and an antibiotic-responsive transcription factor CdeR. In this study, we show that these factors independently modulate the transcription of the antibiotic resistance genes and coordinate to ensure sensitive responses to changes in cell density. The results give new insight into antibiotic resistance regulation inC. subtsugaeand contribute to a broader understanding of how bacteria optimize the regulation of antibiotic resistance in response to changes in the environment.
Structural insight into translation initiation of theλcl leaderless mRNA
Authors: Acosta-Reyes Francisco J. , Bhattacharjee Sayan , Gottesman Max , Frank Joachim 
Published: September 2023

AbstractIn bacteriophageλlysogens, theλcI repressor is encoded by the leaderless transcript (lmRNA) initiated at theλpRM promoter. Translation is enhanced inrpsBmutants deficient in ribosomal protein uS2. Although translation initiation of lmRNA is conserved in bacteria, archaea, and eukaryotes, structural insight of a lmRNA translation initiation complex is missing. Here, we use cryo-EM to solve the structures of the uS2-deficient 70S ribosome of hostE. colimutantrpsB11and the wild-type 70S complex withλcI lmRNA and fmet-tRNAfMet. Importantly, the uS2-deficient 70S ribosome also lacks protein bS21. The anti-Shine-Dalgarno (aSD) region is structurally supported by bS21, so that the absence of the latter causes the aSD to divert from the normal mRNA exit pathway, easing the exit of lmRNA. A π-stacking interaction between the monitor base A1493 and A(+4) of lmRNA potentially acts as a recognition signal. Coulomb charge flow, along with peristalsis-like dynamics within the mRNA entry channel due to the increased 30S head rotation caused by the absence of uS2, are likely to facilitate the propagation of lmRNA through the ribosome. These findings lay the groundwork for future research on the mechanism of translation and the co-evolution of lmRNA and mRNA that includes the emergence of a defined ribosome-binding site of the transcript.
The type of DNA damage response after Decitabine treatment depends on the level of DNMT activity
Authors: Aumer Tina , Bergmayr Linda , Kartika Stephanie , Zeng Theodor , Ge Qingyi , Giorgio Grazia , Däther Maike , Hess Alexander J. , Michalakis Stylianos , Traube Franziska R. 
Published: September 2023

ABSTRACTDecitabine and Azacytidine are considered as epigenetic drugs that induce DNA- methyltransferase (DNMT)-DNA crosslinks, resulting in DNA-hypomethylation and -damage. Although they are applied against myeloid cancers, important aspects of their mode of action remain unknown, which highly limits their clinical potential. Using a combinatorial approach, we reveal that the efficacy profile of both compounds primarily depends on the level of induced DNA-damage. Under low DNMT-activity, only Decitabine has a substantial impact. Conversely, when DNMT-activity is high, toxicity and cellular response to both compounds are dramatically increased, but do not primarily depend on DNA-hypomethylation or RNA-associated processes, contradicting an RNA-dependent effect of Azacytidine. By applying spatial proteomics, we show that Decitabine induces a strictly DNMT-dependent multifaceted DNA- damage response based on chromatin-recruitment of various repair-associated proteins. The choice of DNA-repair pathway herby depends on the severity of Decitabine-induced DNA- lesions. While mismatch (MMR) and base-excision DNA repair (BER) as well as RAD50- dependent DNA double-strand break repair are always activated in response to Decitabine, Fanconi anemia-dependent DNA-repair combined with homologous recombination is only activated when DNMT-activity is moderate. In contrast, high DNMT-activity and therefore immense replication stress, induce DNA repair by non-homologous and alternative end-joining.
Patchy and widespread distribution of bacterial translation arrest peptides associated with the protein localization machinery
Authors: Fujiwara Keigo , Tsuji Naoko , Yoshida Mayu , Takada Hiraku , Chiba Shinobu 
Published: September 2023

AbstractRegulatory arrest peptides exert cellular functions via mechanisms involving regulated translational arrest. Monitoring substrates, a class of arrest peptides, feedback-regulate the expression of the Sec or YidC protein localization machinery. Previously, only a limited number of monitoring substrates were identified. In this study, we performed a bacterial domain-wide search, followed byin vivoandin vitroanalyses, leading to a comprehensive identification of many novel Sec/YidC-related arrest peptides that showed patchy, but widespread, phylogenetic distribution throughout the bacterial domain. Identification of five novel arrest-inducing sequences suggests that bacteria have evolved various arrest-inducing mechanisms. We also identified many arrest peptides that share an R-A-P-P like sequence, suggesting that this sequence could serve as a common evolutionary seed that could overcome the species-specific structures of ribosomes, to evolve arrest peptides. Our comprehensive phylogenetic study revealed that arrest peptide is a prevalent mechanism for the gene regulation of the protein localization machinery.
Small RNAs from Mitochondrial Genome Recombination Sites are Incorporated intoT. gondiiMitoribosomes
Authors: Tetzlaff Sabrina , Hillebrand Arne , Drakoulis Nikiforos , Gluhic Zala , Maschmann Sascha , Lyko Peter , Wicke Susann , Schmitz-Linneweber Christian 
Published: September 2023

AbstractThe mitochondrial genomes of apicomplexans comprise merely three protein-coding genes, alongside a set of thirty to forty genes encoding small RNAs (sRNAs), many of which exhibit homologies to rRNA fromE. coli. The expression status and integration of these short RNAs into ribosomes remains unclear and direct evidence for active ribosomes within apicomplexan mitochondria is still lacking. In this study, we conducted small RNA sequencing on the apicomplexanToxoplasma gondiito investigate the occurrence and function of mitochondrial sRNAs. To enhance the analysis of sRNA sequencing outcomes, we also re-sequenced theT. gondiimitochondrial genome using an improved organelle enrichment protocol and Nanopore sequencing. It has been established previously that theT. gondiigenome comprises 21 sequence blocks that undergo recombination among themselves but that their order is not entirely random. The enhanced coverage of the mitochondrial genome allowed us to characterize block combinations at increased resolution. Employing this refined genome for sRNA mapping, we find that many small RNAs originated from the junction sites between protein-coding blocks and rRNA sequence blocks. Surprisingly, such block border sRNAs were incorporated into polysomes together with canonical rRNA fragments and mRNAs. In conclusion, apicomplexan ribosomes are active within polysomes and are indeed assembled through the integration of sRNAs, including previously undetected sRNAs with merged mRNA-rRNA sequences. Our findings lead to the hypothesis thatT. gondii’sblock-based genome organization enables the dual utilization of mitochondrial sequences as both messenger RNAs and ribosomal RNAs, potentially establishing a link between the regulation of rRNA and mRNA expression.