Comparative in Silico Analyses of Cpeb1–4 with Functional Predictions

Background Cytoplasmic polyadenylation element binding proteins (Cpebs) are a family of proteins that bind to defined groups of mRNAs and regulate their translation. While Cpebs were originally identified as important features of oocyte maturation, recent interest is due to their prospective roles in neural system plasticity. Results In this study we made use of bioinformatic tools and methods including NCBI Blast, UCSC Blat, and Invitrogen Vector NTI to comprehensively analyze all known isoforms of four mouse Cpeb paralogs extracted from the national UniGene, UniProt, and NCBI protein databases. We identified multiple alternative splicing variants for each Cpeb. Regions of commonality and distinctiveness were evident when comparing Cpeb2, 3, and 4. In addition, we performed cross-ortholog comparisons among multiple species. The exon patterns were generally conserved across vertebrates. Mouse and human isoforms were compared in greater detail as they are the most represented in the current databases. The homologous and distinct regions are strictly conserved in mouse Cpeb and human CPEB proteins. Novel variants were proposed based on cross-ortholog comparisons and validated using biological methods. The functions of the alternatively spliced regions were predicted using the Eukaryotic Linear Motif resource. Conclusions Together, the large number of transcripts and proteins indicate the presence of a hitherto unappreciated complexity in the regulation and functions of Cpebs. The evolutionary retention of variable regions as described here is most likely an indication of their functional significance.

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Short linear motif acquisition, exon formation and alternative splicing determine a pathway to diversity for NCoR-family co-repressors

Open Biology ◽

10.1098/rsob.150063 ◽

2015 ◽

Vol 5 (8) ◽

pp. 150063 ◽

Cited By ~ 6

Author(s):

Stephen Short ◽

Tessa Peterkin ◽

Matthew Guille ◽

Roger Patient ◽

Colin Sharpe

Keyword(s):

Alternative Splicing ◽

Gene Sequence ◽

Species Differences ◽

Single Point ◽

Stem Cell Differentiation ◽

Single Point Mutation ◽

Linear Motif ◽

Cellular Context ◽

Alternatively Spliced ◽

Linear Motifs

Vertebrate NCoR-family co-repressors play central roles in the timing of embryo and stem cell differentiation by repressing the activity of a range of transcription factors. They interact with nuclear receptors using short linear motifs (SLiMs) termed co-repressor for nuclear receptor (CoRNR) boxes. Here, we identify the pathway leading to increasing co-repressor diversity across the deuterostomes. The final complement of CoRNR boxes arose in an ancestral cephalochordate, and was encoded in one large exon; the urochordates and vertebrates then split this region between 10 and 12 exons. In Xenopus , alternative splicing is prevalent in NCoR2, but absent in NCoR1. We show for one NCoR1 exon that alternative splicing can be recovered by a single point mutation, suggesting NCoR1 lost the capacity for alternative splicing. Analyses in Xenopus and zebrafish identify that cellular context, rather than gene sequence, predominantly determines species differences in alternative splicing. We identify a pathway to diversity for the NCoR family beginning with the addition of a SLiM, followed by gene duplication, the generation of alternatively spliced isoforms and their differential deployment.

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How to Annotate and Submit a Short Linear Motif to the Eukaryotic Linear Motif Resource

Methods in Molecular Biology - Intrinsically Disordered Proteins ◽

10.1007/978-1-0716-0524-0_4 ◽

2020 ◽

pp. 73-102

Author(s):

Marc Gouw ◽

Jesús Alvarado-Valverde ◽

Jelena Čalyševa ◽

Francesca Diella ◽

Manjeet Kumar ◽

...

Keyword(s):

Linear Motif ◽

Eukaryotic Linear Motif

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The Eukaryotic Linear Motif Resource (ELM): Regulatory Sites in Proteins

Nature Precedings ◽

10.1038/npre.2009.3152.1 ◽

2009 ◽

Author(s):

Francesca Diella ◽

Allegra Via ◽

Claudia Chica ◽

Katja Luck ◽

Catherin Gould ◽

...

Keyword(s):

Linear Motif ◽

Eukaryotic Linear Motif ◽

Regulatory Sites

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Mutator-Like Element in the Yeast Yarrowia lipolytica Displays Multiple Alternative Splicings

Eukaryotic Cell ◽

10.1128/ec.4.3.615-624.2005 ◽

2005 ◽

Vol 4 (3) ◽

pp. 615-624 ◽

Cited By ~ 27

Author(s):

Cécile Neuvéglise ◽

Fabienne Chalvet ◽

Patrick Wincker ◽

Claude Gaillardin ◽

Serge Casaregola

Keyword(s):

Amino Acids ◽

Yarrowia Lipolytica ◽

Base Change ◽

Open Reading Frames ◽

Splice Sites ◽

Protein Coding ◽

Reverse Transcription Pcr ◽

Multiple Alternative ◽

Alternatively Spliced ◽

New Type

ABSTRACT A new type of DNA transposon, Mutyl, has been identified in the sequenced genome of the yeast Yarrowia lipolytica. This transposon is 7,413 bp long and carries two open reading frames (ORFs) which potentially encode proteins of 459 and 1,178 amino acids, respectively. Whereas the first ORF shows no significant homology to previously described proteins, the second ORF shows sequence similarities with various Mutator-like element (MULE)-encoded transposases, including the bacterial transposase signature sequence. Other MULE features shared by Mutyl include a zinc finger motif in the putative transposase, a 22-bp-long imperfect inverted repeat at each end, and a 9- to 10-bp duplication of its target site in the chromosome. Of the five copies of Mutyl present in the genome, one has a deletion of the first 8 bases, and the others are full length with a single base change in one element. The first potential gene of Mutyl, mutB, was shown to be expressed in exponentially growing cells. Its sequence contains a predicted intron with two 5′ splice sites, a single branch point, and two 3′ splice sites. Its mRNA is alternatively spliced, as judged by reverse transcription-PCR, and generates four mRNAs corresponding to protein-coding sequences of 128, 156, 161, and 190 amino acids. Of the three distinct lineages characterized in Y. lipolytica, strains from the German lineage and the French lineage do not carry Mutyl. A study of the distribution of Mutyl in strains of the French lineage evidenced a recent transposition event. Taken together, these results indicate that Mutyl is still active.

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BEM46 Shows Eisosomal Localization and Association with Tryptophan-Derived Auxin Pathway in Neurospora crassa

Eukaryotic Cell ◽

10.1128/ec.00061-14 ◽

2014 ◽

Vol 13 (8) ◽

pp. 1051-1063 ◽

Cited By ~ 9

Author(s):

K. Kollath-Leiß ◽

C. Bönniger ◽

P. Sardar ◽

F. Kempken

Keyword(s):

Neurospora Crassa ◽

Fluorescent Protein ◽

Developmental Stages ◽

Yellow Fluorescent Protein ◽

Content Type ◽

Bioinformatic Tools ◽

Ascospore Germination ◽

Alternatively Spliced ◽

Indole Production

ABSTRACTBEM46 proteins are evolutionarily conserved, but their functions remain elusive. We reported previously that the BEM46 protein inNeurospora crassais targeted to the endoplasmic reticulum (ER) and is essential for ascospore germination. In the present study, we established abem46knockout strain ofN. crassa. This Δbem46mutant exhibited a level of ascospore germination lower than that of the wild type but much higher than those of the previously characterizedbem46-overexpressing and RNA interference (RNAi) lines. Reinvestigation of the RNAi transformants revealed two types of alternatively splicedbem46mRNA; expression of either type led to a loss of ascospore germination. Our results indicated that the phenotype was not due tobem46mRNA downregulation or loss but was caused by the alternatively spliced mRNAs and the peptides they encoded. Using theN. crassaortholog of the eisosomal protein PILA fromAspergillus nidulans, we further demonstrated the colocalization of BEM46 with eisosomes. Employing the yeast two-hybrid system, we identified a single interaction partner: anthranilate synthase component II (encoded bytrp-1). This interaction was confirmedin vivoby a split-YFP (yellow fluorescent protein) approach. The Δtrp-1mutant showed reduced ascospore germination and increased indole production, and we used bioinformatic tools to identify a putative auxin biosynthetic pathway. The genes involved exhibited various levels of transcriptional regulation in the differentbem46transformant and mutant strains. We also investigated the indole production of the strains in different developmental stages. Our findings suggested that the regulation of indole biosynthesis genes was influenced bybem46overexpression. Furthermore, we uncovered evidence of colocalization of BEM46 with the neutral amino acid transporter MTR.

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Complex 5′ Genomic Structure of the Human Prolactin Receptor: Multiple Alternative Exons 1 and Promoter Utilization

Endocrinology ◽

10.1210/endo.143.6.8949 ◽

2002 ◽

Vol 143 (6) ◽

pp. 2139-2142 ◽

Cited By ~ 21

Author(s):

Zhang-Zhi Hu ◽

Li Zhuang ◽

Jianping Meng ◽

Chon-Hwa Tsai-Morris ◽

Maria L. Dufau

Keyword(s):

Genomic Structure ◽

Prolactin Receptor ◽

Exon 2 ◽

Multiple Promoters ◽

Exon 1 ◽

Multiple Alternative ◽

Alternatively Spliced ◽

Genomic Regions ◽

Basal Transcriptional Activity ◽

Half Site

Abstract Transcription of the prolactin receptor (PRLR) is under the control of multiple promoters. Following the recent demonstration of the human non-coding exon 1, hE1N (hE1N1) and the generic exon 1 hE13, we have identified their promoters and characterized four other novel human exons 1 (hE1N2–5) that are alternatively spliced to a common non-coding exon 2 in human tissues and breast cancer cells. Genomic regions containing these exons, and 5′-flanking and intronic sequences, were determined and their order was established in chromosome 5p14-13. Promoters utilized in the transcription of previously characterized PRLR exons 1 species hE13 (hPII) and hE1N1 (hPN1) were found to employ distinct mechanisms for controlling hPRLR transcription. hPIII requires C/EBPβ and Sp1/Sp3 for basal transcriptional activity, while hPN1 activity is conferred by domains containing an Ets element and an NR half-site. The complex promoter control system that governs transcription of the hPRLR in multiple tissues is of relevance for studies on the regulation of PRLR expression in physiological and pathological states.

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Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications

Science Signaling ◽

10.1126/scisignal.abd0334 ◽

2021 ◽

Vol 14 (665) ◽

pp. eabd0334 ◽

Cited By ~ 2

Author(s):

Bálint Mészáros ◽

Hugo Sámano-Sánchez ◽

Jesús Alvarado-Valverde ◽

Jelena Čalyševa ◽

Elizabeth Martínez-Pérez ◽

...

Keyword(s):

Molecular Switches ◽

Membrane Dynamics ◽

Cell Entry ◽

Host Cells ◽

Linear Motif ◽

Angiotensin Converting Enzyme 2 ◽

Therapeutic Implications ◽

Peptide Interactions ◽

Linear Motifs ◽

Eukaryotic Linear Motif

The first reported receptor for SARS-CoV-2 on host cells was the angiotensin-converting enzyme 2 (ACE2). However, the viral spike protein also has an RGD motif, suggesting that cell surface integrins may be co-receptors. We examined the sequences of ACE2 and integrins with the Eukaryotic Linear Motif (ELM) resource and identified candidate short linear motifs (SLiMs) in their short, unstructured, cytosolic tails with potential roles in endocytosis, membrane dynamics, autophagy, cytoskeleton, and cell signaling. These SLiM candidates are highly conserved in vertebrates and may interact with the μ2 subunit of the endocytosis-associated AP2 adaptor complex, as well as with various protein domains (namely, I-BAR, LC3, PDZ, PTB, and SH2) found in human signaling and regulatory proteins. Several motifs overlap in the tail sequences, suggesting that they may act as molecular switches, such as in response to tyrosine phosphorylation status. Candidate LC3-interacting region (LIR) motifs are present in the tails of integrin β3 and ACE2, suggesting that these proteins could directly recruit autophagy components. Our findings identify several molecular links and testable hypotheses that could uncover mechanisms of SARS-CoV-2 attachment, entry, and replication against which it may be possible to develop host-directed therapies that dampen viral infection and disease progression. Several of these SLiMs have now been validated to mediate the predicted peptide interactions.

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Emerging data on androgen receptor splice variants in prostate cancer

Endocrine Related Cancer ◽

10.1530/erc-16-0298 ◽

2016 ◽

Vol 23 (12) ◽

pp. T199-T210 ◽

Cited By ~ 25

Author(s):

Subing Cao ◽

Yang Zhan ◽

Yan Dong

Keyword(s):

Prostate Cancer ◽

Androgen Receptor ◽

Splice Variants ◽

Deep Understanding ◽

Castration Resistant Prostate Cancer ◽

Castration Resistant ◽

Splicing Variants ◽

Current Therapies ◽

Alternatively Spliced ◽

Androgen Receptor Splice Variants

Androgen receptor splice variants are alternatively spliced variants of androgen receptor, which are C-terminally truncated and lack the canonical ligand-binding domain. Accumulating evidence has indicated a significant role of androgen receptor splice variants in mediating resistance of castration-resistant prostate cancer to current therapies and in predicting therapeutic responses. As such, there is an urgent need to target androgen receptor splicing variants for more effective treatment of castration-resistant prostate cancer. Identification of precise and critical targeting points to deactivate androgen receptor splicing variants relies on a deep understanding of how they are generated and the mechanisms of their action. In this review, we will focus on the emerging data on their generation, clinical significance and mechanisms of action as well as the therapeutic influence of these findings.

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Metabarcoding with MinION: Speeding up the detection of invasive aquatic species using environmental DNA and nanopore sequencing

ARPHA Conference Abstracts ◽

10.3897/aca.4.e65036 ◽

2021 ◽

Vol 4 ◽

Author(s):

Bastian Egeter ◽

Joana Veríssimo ◽

Manuel Lopes-Lima ◽

catia chaves ◽

Joana Pinto ◽

...

Keyword(s):

Invasive Species ◽

Environmental Dna ◽

Morphological Identification ◽

Nanopore Sequencing ◽

Sequencing Technology ◽

Bioinformatic Tools ◽

Invasive Bivalves ◽

Multiple Species ◽

High Level ◽

Laboratory Protocol

Traditional detection of aquatic invasive species, via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindrances, but sample processing is often lengthy. More recently, portable nanopore sequencing technology has become available, which has the potential to make molecular detection of invasive species more widely accessible and to substantially decrease sample turnaround times. However, nanopore-sequenced reads have a much higher error rate than those produced by Illumina platforms, which has so far hindered the adoption of this technology. We provide a detailed laboratory protocol and bioinformatic tools to increase the reliability of nanopore sequencing to detect invasive species, and we test its application using invasive bivalves. We sampled water from sites with pre-existing bivalve occurrence and abundance data, and contrasting bivalve communities, in Italy and Portugal. We extracted, amplified and sequenced eDNA with a turnaround of 3.5 days. The majority of processed reads were ≥ 99 % identical to reference sequences. There were no taxa detected other than those known to occur. The lack of detections of some species at some sites could be explained by their known low abundances. The approach is now being tested on other target taxa such as fish and other vertebrates.

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