Biology subjects

Karlowski, W. M.

Publications and source records attributed to Karlowski, W. M..

5 recordsLinked to original sources

bioRxiv2023

MiRNAs differentially expressed in vegetative and reproductive organs of Marchantia polymorpha, insights into their expression pattern, gene structures and function

MicroRNAs (miRNAs) regulate gene expression affecting a variety of plant developmental processes. The evolutionary position of Marchantia polymorpha makes it a significant model to understand miRNA-mediated gene regulatory pathways in plants. Previous studies focused on conserved miRNA-target mRNA modules showed their critical role in Marchantia development. Here, we demonstrate that differential expression of conserved miRNAs and their targets in selected organs of Marchantia additionally underlines their role in regulating fundamental developmental processes. The main aim of this study was to characterize selected liverwort-specific miRNAs, as there is a limited knowledge on their biogenesis, accumulation, targets, and function in Marchantia. We demonstrate their differential accumulation in vegetative and generative organs. We reveal that all liverwort-specific miRNAs examined are encoded by independent transcriptional units. MpmiR11737a, MpmiR11887 and MpmiR11796, annotated as being encoded within protein-encoding genes, have their own independent transcription start sites. The analysis of selected liverwort-specific miRNAs and their pri-miRNAs often reveal correlation in their levels, suggesting transcriptional regulation. However, MpmiR11796 shows a reverse correlation to its pri-miRNA level, suggesting post-transcriptional regulation. Moreover, we identify novel targets for selected liverwort-specific miRNAs and demonstrate an inverse correlation between their expression and miRNA accumulation. In the case of one miRNA precursor, we provide evidence that it encodes two functional miRNAs with two independent targets. Overall, our research sheds light on liverwort-specific miRNA gene structure, provides new data on their biogenesis and expression regulation. Furthermore, identifying their targets, we hypothesize the potential role of these miRNAs in early land plant development and functioning.

molecular biology↗

bioRxiv2023

PEP444c encoded within the MIR444c gene regulates microRNA444c accumulation in barley

MicroRNAs are small, non-coding RNA molecules that regulate expression of their target genes. The MIR444 gene family is present exclusively in monocotyledons, and microRNAs444 from this family have been shown to target certain MADS-box transcription factors in rice and barley. We identified three barley MIR444 (MIR444a/b/c) genes and comprehensively characterized their structure and the processing pattern of the primary transcripts (pri-miRNAs444). Pri-microRNAs444 undergo extensive alternative splicing, by which functional and non-functional pri-miRNA444 isoforms are generated. We show that barley pri-miRNAs444 contain numerous open reading frames (ORFs) whose transcripts associate with ribosomes. Using specific antibodies, we provide evidence that selected ORFs encoding PEP444a within MIR444a and PEP444c within MIR444c are expressed in barley plants. Moreover, we demonstrate that CRISPR-associated endonuclease 9 (Cas9)-mediated mutagenesis of the PEP444c encoding sequence results in a decreased level of PEP444 transcript in barley shoots and roots, and a 5-fold reduced level of mature microRNA444c in roots. Taken together, our observations suggest that PEP444c encoded by the MIR444c gene is involved in microRNA444c biogenesis in barley.

plant biology↗

bioRxiv2023

TRGdb: a universal resource for exploration of taxonomically restricted genes in bacteria

The TRGdb database is a resource dedicated to taxonomically restricted genes (TRGs) in bacteria. It provides a comprehensive collection of genes that are specific to different genera and species, according to the latest release of bacterial taxonomy. The user interface allows for easy browsing and searching as well as sequence similarity exploration. The website also provides information on each TRG protein sequence, including its level of disorder, complexity, and tendency to aggregate. TRGdb is a valuable resource for gaining a deeper understanding of the TRGs-associated, unique features and characteristics of bacterial organisms. The TRGdb resource is freely accessible through www.combio.pl/trgdb.

bioinformatics↗

bioRxiv2021

Taxonomy-aware, sequence similarity ranking reliably predicts phage-host relationships

BackgroundSimilar regions in virus and host genomes provide strong evidence for phage-host interaction, and BLAST is one of the leading tools to predict prokaryotic hosts from phage sequences. However, BLAST-based host prediction has three major limitations: (i) top-scoring sequences do not always point to the actual host, (ii) mosaic phage genomes may match to many, typically related, bacteria, and (iii) phage and host sequences may diverge beyond the point where their relationship can be detected by a BLAST alignment. ResultsWe created an extension to BLAST, named Phirbo, that improves host prediction quality beyond what is obtainable from standard BLAST searches. The tool harnesses information concerning sequence similarity and bacteria relatedness to predict phage-host interactions. Phirbo was evaluated on three benchmark sets of known phage-host pairs, and it improved precision and recall by 11-40 percentage points over currently available, state-of-the-art, alignment-based, alignment-free, and machine learning host prediction tools. Moreover, the discriminatory power of Phirbo for the recognition of phage-host relationships surpassed the results of other tools by at least 10 percentage points (Area Under the Curve = 0.95), yielding a mean host prediction accuracy of 57% and 68% at the genus and family levels respectively, and drops by 12 percentage points when using only a fraction of phage genome sequences (3 kb). Finally, we provide insights into a repertoire of protein and ncRNA genes that are shared between phages and hosts and may be prone to horizontal transfer during infection. ConclusionsOur results suggest that Phirbo is a simple and effective tool for predicting phage host relationships.

bioinformatics↗

bioRxiv2019

Benchmarking of alignment-free sequence comparison methods

Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment. Here, we present a community resource (http://afproject.org) to establish standards for comparing alignment-free approaches across different areas of sequence-based research. We characterize 74 AF methods available in 24 software tools for five research applications, namely, protein sequence classification, gene tree inference, regulatory element detection, genome-based phylogenetic inference and reconstruction of species trees under horizontal gene transfer and recombination events. The interactive web service allows researchers to explore the performance of alignment-free tools relevant to their data types and analytical goals. It also allows method developers to assess their own algorithms and compare them with current state-of-the-art tools, accelerating the development of new, more accurate AF solutions.

bioinformatics↗