Andrzej Zielezinski

Andrzej Zielezinski
Adam Mickiewicz University | UAM · Department of Computational Biology

PhD

About

40
Publications
4,783
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719
Citations
Additional affiliations
October 2014 - present
Adam Mickiewicz University
Position
  • Professor (Assistant)

Publications

Publications (40)
Article
Micro RNAs (miRNAs) are small, non-coding endogenous RNA molecules of 18–24 nucleotides in length that control multiple gene regulatory pathways via posttranscriptional gene silencing in eukaryotes. To develop a comprehensive picture of the evolutionary history of miRNA biogenesis and action in land plants, new studies on bryophyte representatives...
Article
Full-text available
PHIST (Phage-Host Interaction Search Tool) predicts prokaryotic hosts of viruses based on exact matches between viral and host genomes. It improves host prediction accuracy at species level over current alignment-based tools (on average by 3 percentage points) as well as alignment-free and CRISPR-based tools (by 14–20 percentage points). PHIST is a...
Article
Full-text available
Background Characterizing phage–host interactions is critical to understanding the ecological role of both partners and effective isolation of phage therapeuticals. Unfortunately, experimental methods for studying these interactions are markedly slow, low-throughput, and unsuitable for phages or hosts difficult to maintain in laboratory conditions....
Preprint
Full-text available
PHIST (Phage-Host Interaction Search Tool) predicts prokaryotic hosts of viruses from their genomic sequences. It improves host prediction accuracy at species level over current alignment-based tools (on average by 3 percentage points) as well as alignment-free and CRISPR-based tools (by 14-20 percentage points). PHIST is also two orders of magnitu...
Article
Full-text available
Culture-independent approaches have recently shed light on the genomic diversity of viruses of prokaryotes. One fundamental question when trying to understand their ecological roles is: which host do they infect? To tackle this issue we developed a machine-learning approach named Random Forest Assignment of Hosts (RaFAH), that uses scores to 43,644...
Preprint
Full-text available
Motivation Similar regions in virus and host genomes provide strong evidence for phage-host interaction, and BLAST is one of the leading tools to predict hosts from phage sequences. However, BLAST-based host prediction has three limitations: (i) top-scoring prokaryotic sequences do not always point to the actual host, (ii) mosaic phage genomes may...
Chapter
Full-text available
MicroRNAs control plant development and are key regulators of plant responses to biotic and abiotic stresses. Thus, their expression must be carefully controlled since both excess and deficiency of a given microRNA may be deleterious to plant cell. MicroRNA expression regulation can occur at several stages of their biogenesis pathway. One of the mo...
Article
Full-text available
Bioinsecticides consisting of different sets of Bacillus thuringiensis (Bt) Cry, Cyt and Vip toxins are broadly used in pest control. Possible interactions (synergistic, additive or antagonistic) between these proteins can not only influence the overall efficacy of certain Bt-based bioinsecticide, but also raise questions regarding environmental sa...
Preprint
Full-text available
Viruses of prokaryotes are extremely abundant and diverse. Culture-independent approaches have recently shed light on the biodiversity these biological entities 1,2 . One fundamental question when trying to understand their ecological roles is: which host do they infect? To tackle this issue we developed a machine-learning approach named Random For...
Article
Full-text available
Glycogen synthase kinase 3 (GSK3) is a highly conserved kinase present in all eukaryotes and functions as a key regulator of a wide range of physiological and developmental processes. The kinase, known in land plants as GSK3/SHAGGY-like kinase (GSK), is a key player in the brassinosteroid (BR) signaling pathway. The GSK genes, through the BRs, affe...
Article
Full-text available
In wheat, adult plant resistance (APR) to leaf rust (Puccinia triticina), is effective in restricting pathogen growth and provides durable resistance against a wide range of virulent forms of P. triticina. Despite the importance, there is limited knowledge on the molecular basis of this type of resistance. We isolated and characterized the wall-ass...
Article
Full-text available
Background: 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. Results: Here, we present a community resource (http://afproject.or...
Preprint
Full-text available
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 standard...
Article
Full-text available
GLYCOGEN SYNTHASE KINASE3/Shaggy-like kinases (GSKs) represent a highly conserved group of proteins found in all eukaryotes. In plants they are encoded by multigene families and integrate signaling of brassinosteroids, auxin and abscisic acid in wide range of physiological and developmental processes with a strong impact on plant responses to envir...
Data
Schematic structure of genomic region of Brachypodium distachyon chromosome1 showing two neighboring genes BRADI1G02150.1 and BRADI1G02160.1. (TIF)
Data
List of GSK-encoding genes in Arabidopsis thaliana and barley. (XLS)
Data
Nucleotide alignment of amplicon A and the corresponding fragment of HORVU5Hr1G119790 gene. Primers used for fragment A amplification (A_Fw and A_Re) and sequencing (C_Re and D_Fw) are highlighted. The region of amplicon A corresponding to amine oxidase encoding transcript (AK357034.1 and AK363738.1) is marked with blue, the region corresponding to...
Data
List of primers and reaction conditions used in this study. (DOCX)
Data
Amino acid alignment of GSK-encoded proteins in Arabidopsis thaliana, barley and Physcomitrella patens. Boundaries of the kinase domain (Pfam AC: PF00069) are indicated by black arrows and framed in black. Alignment includes one protein isoform per gene (isoform containing kinase domain with the highest Pfam score). (DOCX)
Article
tRNA-derived fragments (tRFs) constitute a new class of short regulatory RNAs that are a product of nascent or mature tRNA processing. tRF sequences have been identified in all domains of life; however, most published research pertains to human, yeast and some bacterial organisms. Despite growing interest in plant tRFs and accumulating evidence of...
Article
Full-text available
Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. The strength of these methods makes them particularly useful for next-generation sequencing data processing and analysi...
Chapter
WG/GW domains recruit ARGONAUTE (AGO) proteins to distinct silencing effector complexes using combinations of just two amino acids: tryptophan (W) and glycine (G), forming a wide arsenal of highly simplified interaction surfaces. These unstructured domains exhibit very low sequence identity and excessive length polymorphism, which makes identificat...
Article
Full-text available
ORCAN (ORtholog sCANner) is a web-based meta-server for one-click evolutionary and functional annotation of protein sequences. The server combines information from the most popular orthology-prediction resources, including four tools and four online databases. Functional annotation utilizes five additional comparisons between the query and identifi...
Article
Nicotine may affect cell function by rearranging protein complexes. We aimed to determine nicotine-induced alterations of protein complexes in Caenorhabditis elegans (C. elegans) cells, thereby revealing links between nicotine exposure and protein complex modulation. We compared the proteomic alterations induced by low and high nicotine concentrati...
Article
Full-text available
Ribosomal 5S RNA (5S rRNA) is the ubiquitous RNA component found in the large subunit of ribosomes in all known organisms. Due to its small size, abundance and evolutionary conservation 5S rRNA for many years now is used as a model molecule in studies on RNA structure, RNA–protein interactions and molecular phylogeny. 5SRNAdb (http://combio.pl/5srn...
Article
Full-text available
MicroRNAs are the key post-transcriptional regulators of gene expression in development and stress responses. Thus, precisely quantifying the level of each particular microRNA is of utmost importance when studying the biology of any organism. The mirEX 2.0 web portal ( http://www.combio.pl/mirex ) provides a comprehensive platform for the explorati...
Article
Full-text available
The GW182 proteins are a key component of the miRNA-dependent post-transcriptional silencing pathway in animals. They function as scaffold proteins to mediate the interaction of Argonaute (AGO)-containing complexes with cytoplasmic poly(A)-binding proteins (PABP) and PAN2-PAN3 and CCR4-NOT deadenylases. The AGO-GW182 complexes mediate silencing of...
Article
Full-text available
The narrow-leafed lupin (Lupinus angustifolius) was recently considered as a legume reference species. Genetic resources have been developed, including a draft genome sequence, linkage maps, nuclear DNA libraries, and cytogenetic chromosome-specific landmarks. Here, we used a complex approach, involving DNA fingerprinting, sequencing, genetic mappi...
Article
Full-text available
Motivation: Argonaute-interacting WG/GW proteins are characterized by the presence of repeated sequence motifs containing glycine (G) and tryptophan (W). The motifs seem to be remarkably adaptive to amino acid substitutions and their sequences show non-contiguity. Our previous approach to the detection of GW domains, based on scoring their gross a...
Article
Full-text available
mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data. RT–qPCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. A new way of accessing gene expression data in mirEX includes a simple mouse operated querying system and...
Article
Full-text available
We present here a highly portable and easy-to-use gene annotation system CEL (Computational Environment for annotation of Legume genomes) that can be used to annotate any type of genomic sequence -- from BAC ends to complete chromosomes. CEL's core engine is modular and hierarchically organized with an open-source structure, permitting maximum cust...
Article
Full-text available
AGO(Argonaute)-binding domains, composed of repeated motifs, in which only binary combinations of tryptophan and glycine are conserved, bind AGO proteins and are essential during RNAi-mediated gene silencing. The amino acid sequence of this domain is extremely divergent and therefore very difficult to detect. Commonly used bioinformatic tools fail...
Article
Full-text available
Domains in Arabidopsis proteins NRPE1 and SPT5-like, composed almost exclusively of repeated motifs in which only WG or GW sequences and an overall amino-acid preference are conserved, have been experimentally shown to bind multiple molecules of Argonaute (AGO) protein(s). Domain swapping between the WG/GW domains of NRPE1 and the human protein GW1...

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