Pere Puigbo

University of Turku | UTU · Department of Biology

The bone extracellular matrix (ECM) contains minerals deposited on highly crosslinked collagen fibrils and hundreds of non-collagenous proteins. Some of these proteins are key to the regulation of bone formation and regeneration via signaling pathways, and play important regulatory and structural roles. However, the complete list of bone extracellu...

Pollinator decline is one of the gravest challenges facing the world today, and the overuse of pesticides may be among its causes. Here we studied whether glyphosate, the world's most widely used pesticide, affects the bumblebee gut microbiota. We exposed the bumblebee diet to glyphosate and a glyphosate-based herbicide and quantified the microbiot...

Mutation research is crucial for detecting and treating SARS-CoV-2 and developing vaccines. Using over 5,300,000 sequences from SARS-CoV-2 genomes and custom Python programs, we analyzed the mutational landscape of SARS-CoV-2. Although almost every nucleotide in the SARS-CoV-2 genome has mutated at some time, the substantial differences in the freq...

The bone extracellular matrix (ECM) contains minerals deposited on highly crosslinked collagen fibrils and hundreds of non-collagenous proteins. Some of these proteins are key to the regulation of bone formation and regeneration via signaling pathways, and play important regulatory and structural roles. However, the complete list of bone extracellu...

Aims: In a field study, the effects of treatments of glyphosate-based herbicides (GBHs) in soil, alone and in combination with phosphate fertilizer, were examined on the performance and endophytic microbiota of garden strawberry. Methods and results: The root and leaf endophytic microbiota of garden strawberries grown in GBH-treated and untreate...

Predicting SARS-CoV-2 mutations is difficult, but predicting recurrent mutations driven by the host, such as those caused by host deaminases, is feasible. We used machine learning to predict which positions from the SARS-CoV-2 genome will hold a recurrent mutation and which mutations will be the most recurrent. We used data from April 2021 that we...

Non-target organisms are globally exposed to herbicides. While many herbicides - for example, glyphosate - were initially considered safe, increasing evidence demonstrates that they have profound effects on ecosystem functions via altered microbial communities. We provide a comprehensive framework on how herbicide residues may modulate ecosystem-le...

The 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) is the central enzyme of the shikimate pathway to synthesize the three aromatic amino acids in fungi, plants, and prokaryotes. This enzyme is the target of the herbicide glyphosate. In most plants and prokaryotes, the EPSPS protein is constituted by a single domain family, the EPSP synthase (P...

Glyphosate is the world’s most widely used agrochemical. Its use in agriculture and gardening has been proclaimed safe because humans and other animals do not have the target enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). However, increasing numbers of studies have demonstrated risks to humans and animals because the shikimate metaboli...

The genome hypothesis postulates that genes in a genome tend to conform to their species’ usage of the codon catalog and the GC content of the DNA. Thus, codon frequencies differ across organisms, including the three termination codons in the standard genetic code. Here, we analyze the frequencies of stop codons in a group of highly expressed genes...

Glyphosate-based products (GBP) are the most common broad-spectrum herbicides worldwide. The target of glyphosate is the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) in the shikimate pathway, which is virtually universal in plants. The inhibition of the enzyme stops the production of three essential amino acids: phenylalanine, tyrosin...

Glyphosate-based products (GBP) are the most common broad-spectrum herbicides worldwide. The target of glyphosate is the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) in the shikimate pathway, which is virtually universal in plants. The inhibition of the enzyme stops the production of three essential amino acids: phenylalanine, tyrosin...

Stress disorders have dramatically increased in recent decades becoming the most prevalent psychiatric disorder in the United States and Europe. However, the diagnosis of stress disorders is currently based on symptom checklist and psychological questionnaires, thus making the identification of candidate biomarkers necessary to gain better insights...

Early characterization of emerging viruses is essential to control their spread, such as the Zika Virus outbreak in 2014. Among other non-viral factors, host information is essential for the surveillance and control of virus spread. Flaviviruses (genus Flavivirus), akin to other viruses, are modulated by high mutation rates and selective forces to...

Obesity is one of the most incident and concerning disease worldwide. Definite strategies to prevent obesity and related complications remain elusive. Among the risk factors of the onset of obesity, gut microbiota might play an important role in the pathogenesis of the disease, and it has received extensive attention because it affects the host met...

This poster describes the potential effects of the world-widely used herbicide glyphosate on the human gut microbiota. Published in AAAS 2021. See also: Classification of the glyphosate target enzyme (5-enolpyruvylshikimate-3-phosphate synthase) for assessing sensitivity of organisms to the herbicide (DOI: 10.1016/j.jhazmat.2020.124556).

Glyphosate is the leading herbicide worldwide, but it also affects prokaryotes because it targets the central enzyme (5-enolpyruvylshikimate-3-phosphate, EPSP) of the shikimate pathway in the synthesis of the three essential aromatic amino acids in bacteria, fungi and plants. Our results reveal that bacteria may easily become resistant to glyphosat...

Glyphosate is the most common broad-spectrum herbicide. It targets the key enzyme of the shikimate pathway, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), which synthesizes three essential aromatic amino acids (phenylalanine, tyrosine and tryptophan) in plants. Because the shikimate pathway is also found in many prokaryotes and fungi, the wid...

Glyphosate is the leading herbicide worldwide, but it also affects prokaryotes because it targets the central enzyme (EPSPS) of the shikimate pathway in the synthesis of the three essential aromatic amino acids in autotrophs. Our results reveal that bacteria easily become resistant to glyphosate through changes in the EPSPS active site. This indica...

Glyphosate is the most common broad-spectrum herbicide. It targets the key enzyme of the shikimate pathway, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), which synthesizes three essential aromatic amino acids (phenylalanine, tyrosine and tryptophan) in plants. Because the shikimate pathway is also found in many prokaryotes and fungi, the wid...

Early characterization is essential to control the spread of emerging viruses, such as the Zika Virus outbreak in 2014. A major challenge is the identification of potential hosts for novel viruses. We introduce an algorithm to identify the host range of a virus from its raw genome sequence that will be a useful tool to understand host-virus relatio...

Genome-wide comparison of phylogenetic trees is becoming an increasingly common approach in evolutionary genomics, and a variety of approaches for such comparison have been developed. In this article we present several methods for comparative analysis of large numbers of phylogenetic trees. To compare phylogenetic trees taking into account the boot...

Recent studies suggest that exercise alters the gut microbiome. We determined whether six-weeks endurance exercise, without changing diet, affected the gut metagenome and systemic metabolites of overweight women. Previously sedentary overweight women (n = 19) underwent a six-weeks endurance exercise intervention, but two were excluded due to antibi...

Background Evolution of bacterial and archaeal genomes is a highly dynamic process that involves intensive loss of genes as well as gene gain via horizontal transfer, with a lesser contribution from gene duplication. The rates of these processes can be estimated by comparing genomes that are linked by an evolutionary tree. These estimated rates of...

Zika virus is a mosquito-borne Flavivirus that was first discovered in Uganda in 1947, from where it spread along the Equator through Asia. The first report of the virus in South America was in Easter Island (Chile) in 2014. Zika virus has been a major widespread pathogen in South America since early 2015. Currently, Zika viruses can be divided int...

Almost all cellular life forms are hosts to diverse genetic parasites with various levels of autonomy including plasmids, transposons and viruses. Theoretical modeling of the evolution of primordial replicators indicates that parasites (‘cheaters’) necessarily evolve in such systems and can be kept at bay primarily via compartmentalization. Given t...

GPT (Global Positioning Trees) is a web-server that maps phylogenetic trees on a virtual globe. The minimum requirements are a phylogenetic tree and geographical coordinates of leaves to generate a Keyhole Markup Language (KML) file that can be viewed on Google Earth. An advantage of GPT is the results may be pre-visualized directly on the web. Thi...

GPT (Global Positioning Trees) is a web-server that maps phylogenetic trees on a virtual globe. The minimum requirements are a phylogenetic tree and geographical coordinates of leaves to generate a Keyhole Markup Language (KML) file that can be viewed on Google Earth. An advantage of GPT is the results may be pre-visualized directly on the web. Thi...

Genomes of bacteria and archaea (collectively, prokaryotes) appear to exist in incessant flux, expanding via horizontal gene transfer and gene duplication, and contracting via gene loss. However, the actual rates of genome dynamics and relative contributions of different types of event across the diversity of prokaryotes are largely unknown, as are...

Three classes of low-G+C Gram-positive bacteria (Firmicutes), Bacilli, Clostridia and Negativicutes, include numerous members that are capable of producing heat-resistant endospores. Spore-forming firmicutes include many environmentally important organisms, such as insect pathogens and cellulose-degrading industrial strains, as well as human pathog...

Archaeal and bacterial ribosomes contain more than 50 proteins, including 34 that are universally conserved in the three domains of cellular life (bacteria, archaea, and eukaryotes). Despite the high sequence conservation, annotation of ribosomal (r-) protein genes is often difficult because of their short lengths and biased sequence composition. W...

Representative genomes for archaea, bacteria and eukaryotes. (XLS)

Newick-formatted tree shown on Figure 5. (TXT)

Newick-formatted tree shown on Figure 7. (TXT)

Distribution of bacterial r-proteins among genome partitions. (XLS)

Newick-formatted tree shown on Figure 2. (TXT)

Distribution of paralogous r-proteins in bacteria. (PDF)

Phyletic distribution of ribosomal proteins collected in this study. (XLS)

List of bacterial genomes having Thx peptide and multiple alignment of bacterial Thx peptides. (PDF)

List of r-proteins analyzed in this study. (XLS)

List of bacterial and archaeal genomes analyzed in this study. (XLS)

List bacterial and archaeal ribosomal proteins that were missing or misannotated in Refseq database. (XLS)

Detailed comparison of of the pattern of archaeal r-protein gain and loss with Desmond et al., 2011 [18]. (PDF)

Supporting information on phylogenetic analysis. (PDF)

Genome-wide comparison of phylogenetic trees is becoming an increasingly common approach in evolutionary genomics, and a variety of approaches for such comparison have been developed. In this article, we present several methods for comparative analysis of large numbers of phylogenetic trees. To compare phylogenetic trees taking into account the boo...

Proteorhodopsin phototrophy is expected to have considerable impact on the ecology and biogeochemical roles of marine bacteria. However, the genetic features contributing to the success of proteorhodopsin-containing bacteria remain largely unknown. We investigated the genome of Dokdonia sp. strain MED134 (Bacteroidetes) for features potentially exp...

Here, we address the question of why the influenza A virus hemagglutinin (HA) does not escape immunity by hyperglycosylation. Uniquely among dozens of monoclonal antibodies specific for A/Puerto Rico/8/34, escape from H28-A2 neutralization requires substitutions introducing N-linked glycosylation at residue 131 or 144 in the globular domain. This e...

The computational education of biologists is changing to prepare students for facing the complex datasets of today's life science research. In this concise textbook, the authors' fresh pedagogical approaches lead biology students from first principles towards computational thinking. A team of renowned bioinformaticians take innovative routes to int...

The widespread exchange of genes among prokaryotes, known as horizontal gene transfer (HGT), is often considered to "uproot" the Tree of Life (TOL). Indeed, it is by now fully clear that genes in general possess different evolutionary histories. However, the possibility remains that the TOL concept can be reformulated and remain valid as a statisti...

Data for FI. (0.06 MB DOC)

Representation of the first and second components of the Principal Components Analysis (PCA) for H1 viruses. PCA of the amino acids composition of H1N1. The first two components of the PCA account for 59% of the total variability. a) PCA plot by host. Blue diamonds correspond to sequences found in avian viruses, green triangles correspond to sequen...

Flow Chart of Flow Index algorithm. (0.65 MB TIF)

Author Summary Influenza A virus is highly susceptible to neutralizing antibodies specific for the viral hemagglutinin glycoprotein (HA), and is easily controlled by standard vaccines. Influenza A virus remains an important human pathogen, however, due to its ability to rapidly evade antibody responses. This process, termed antigenic drift, is due...

Phylogenetic trees of individual genes of prokaryotes (archaea and bacteria) generally have different topologies, largely owing to extensive horizontal gene transfer (HGT), suggesting that the Tree of Life (TOL) should be replaced by a "net of life" as the paradigm of prokaryote evolution. However, trees remain the natural representation of the his...

The Relative Codon Deoptimization Index (RCDI) was developed by Mueller et al. (2006) as measure of codon deoptimization by comparing how similar is the codon usage of a gene and the codon usage of a reference genome. RCDI/eRCDI is a web application server that calculates the Relative Codon Deoptimization Index and a new expected value for the RCDI...

Extensive horizontal gene transfer (HGT) among prokaryotes seems to undermine the tree of life (TOL) concept. However, the possibility remains that the TOL can be salvaged as a statistical central trend in the phylogenetic "forest of life" (FOL). A comprehensive comparative analysis of 6901 phylogenetic trees for prokaryotic genes revealed a signal...

Comparative genomics has revealed extensive horizontal gene transfer among prokaryotes, a development that is often considered to undermine the 'tree of life' concept. However, the possibility remains that a statistical central trend still exists in the phylogenetic 'forest of life'. A comprehensive comparative analysis of a 'forest' of 6,901 phylo...

A list of species (59 bacterial and 41 archaeal) used for the FOL construction.

All the phylogenetic trees

A list of the 102 COGs that are represented in at least 90 of the100 selected archaea and bacteria.

The Codon Adaptation Index (CAI) was first developed to measure the synonymous codon usage bias for a DNA or RNA sequence. The CAI quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon frequency of a reference set. We describe here CAIcal, a web-server available at http://genomes.urv.es/CAIcal that includes...

The Codon Adaptation Index (CAI) is a measure of the synonymous codon usage bias for a DNA or RNA sequence. It quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon frequency of a reference set. Extreme values in the nucleotide or in the amino acid composition have a large impact on differential preference...

We studied the evolution of thermophily in prokaryotes using the phylogenetic relationships between 279 bacteria and archaea and their thermophilic amino acid composition signature. Our findings suggest several examples in which the capacity of thermophilic adaptation has been gained or lost over relatively short evolutionary periods throughout the...

The highly expressed genes database (HEG-DB) is a genomic database that includes the prediction of which genes are highly expressed in prokaryotic complete genomes under strong translational selection. The current version of the database contains general features for almost 200 genomes under translational selection, including the correspondence ana...