Biology subjects

Eravci, M.

Publications and source records attributed to Eravci, M..

4 recordsLinked to original sources

bioRxiv2022

S. pombe Rtf2 is Important for Replication Fork Barrier Activity of RTS1 via Splicing of Rtf1

Arrested replication forks, when restarted by homologous recombination, result in error-prone DNA syntheses and non-allelic homologous recombination. Fission yeast RTS1 is a model fork barrier used to probe mechanisms of recombination-dependent restart. RTS1 barrier activity is entirely dependent on the DNA binding protein Rtf1 and partially dependent on a second protein, Rtf2. Human RTF2 was recently implicated in fork restart, leading us to examine fission yeast Rtf2s role in more detail. In agreement with previous studies, we observe reduced barrier activity upon rtf2 deletion. However, we identified Rtf2 to be physically associated with mRNA processing and splicing factors and rtf2 deletion to cause increased intron retention. One of the most affected introns resided in the rtf1 transcript. Using an intronless rtf1 we observed no reduction in RFB activity in the absence of Rtf2. Thus, Rtf2 is essential for correct rtf1 splicing to allow optimal RTS1 barrier activity.

genetics↗

bioRxiv2021

Histone acetyltransferase activity of CREB-binding protein is essential for synaptic plasticity in Lymnaea

In eukaryotes, CREB-binding protein (CBP), a coactivator of CREB, functions both as a platform for recruiting other components of the transcriptional machinery and as a histone acetyltransferase (HAT) that alters chromatin structure. We previously showed that the transcriptional activity of cAMP-responsive element binding protein (CREB) plays a crucial role in neuronal plasticity in the pond snail Lymnaea stagnalis. However, there is no information on the role CBP plays in CREB-initiated plastic changes in Lymnaea. In this study, we characterized the Lymnaea CBP (LymCBP) gene and investigated the roles it plays in synaptic plasticity involved in regulating feeding behaviors. Similar to CBPs of other species, LymCBP possesses functional domains, such as KIX domain, which is essential for interaction with CREB and was shown to regulate long-term memory (LTM). In situ hybridization showed that the staining patterns of LymCBP mRNA in the central nervous system were very similar to those of Lymnaea CREB1 (LymCREB1). A particularly strong LymCBP mRNA signal was observed in the Cerebral Giant Cell (CGC), an identified extrinsic modulatory interneuron of the feeding circuit, key to both appetitive and aversive LTM for taste. Biochemical experiments using the recombinant protein of LymCBP HAT domain showed that its enzymatic activity was blocked by classical HAT inhibitors such as curcumin, anacardic acid and garcinol. Preincubation of Lymnaea CNSs with these HAT inhibitors blocked cAMP-induced long-term potentiation between the CGC and the follower B1 motoneuron. We therefore suggest that HAT activity of LymCBP in the CGCs is a key factor in synaptic plasticity contributing to LTM after classical conditioning.

neuroscience↗

bioRxiv2021

A proteomics database for CNS proteins of the great pond snail Lymnaea stagnalis

Applications of key technologies in biomedical research, such as qRT-PCR or LC-MS based proteomics, are generating large biological (-omics) data sets which are useful for the identification and quantification of biomarkers involved in molecular mechanisms of any research area of interest. Genome, transcriptome and proteome databases are already available for a number of model organisms including vertebrates and invertebrates. However, there is insufficient information available for protein sequences of certain invertebrates, such as the great pond snail Lymnaea stagnalis, a model organism that has been used highly successfully in elucidating evolutionarily conserved mechanisms of learning and memory, ageing and age-related as well as amyloid-{beta} induced memory decline. In this investigation, we used a bioinformatics approach to designing and benchmarking a comprehensive CNS proteomics database (LymCNS-PDB) for the identification of proteins from the Central Nervous System (CNS) of Lymnaea stagnalis by LC-MS based proteomics. LymCNS-PDB was created by using the Trinity TransDecoder bioinformatics tool to translate amino acid sequences from mRNA transcript assemblies obtained from an existing published Lymnaea stagnalis transcriptomics database. The blast-style MMSeq2 software was used to match all translated sequences to sequences for molluscan proteins (including Lymnaea stagnalis and other molluscs) available from UniProtKB. LymCNS-PDB, which contains 9,628 identified matched proteins, was then benchmarked by performing LC-MS based proteomics analysis with proteins isolated from the CNS of Lymnaea stagnalis. MS/MS analysis using the LymCNS-PDB database led to the identification of 3,810 proteins while only 982 proteins were identified by using a non-specific Molluscan database. LymCNS-PDB provides a valuable tool that will enable us to perform quantitative proteomics analysis to identify a plethora of protein interactomes involved in several CNS functions in Lymnaea stagnalis including learning and memory, aging-related memory decline and others.

bioinformatics↗

bioRxiv2019

Non-lethal oxidative stress boosts bacterial survival and evolvability under lethal exposure

Unicellular organisms have the prevalent challenge to survive under oxidative stress of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2). ROS are present as by-products of photosynthesis and aerobic respiration. These reactive species are even employed by multicellular organisms as potent weapons against microbes. Although bacterial defences against lethal and sub-lethal oxidative stress have been studied in model bacteria, the role of fluctuating H2O2 concentrations remains unexplored. It is known that sub-lethal exposure of Escherichia coli to H2O2 results in enhanced survival upon subsequent exposure. Here we investigate the priming response to H2O2 at physiological concentrations. The basis and the duration of the response (memory) were also determined by time-lapse quantitative proteomics. We found that a low level of H2O2 induced several scavenging enzymes showing a long half-life, subsequently protecting cells from future exposure. We then asked if the phenotypic resistance against H2O2 alters the evolution of resistance against oxygen stress. Experimental evolution of H2O2 resistance revealed faster evolution and higher levels of resistance in primed cells. Several mutations were found to be associated with resistance in evolved populations affecting different loci but, counterintuitively, none of them was directly associated with scavenging systems. Our results have important implications for host colonisation and infections where microbes often encounter reactive oxygen species in gradients.

evolutionary biology↗