Vassiliki Lila Koumandou

Vassiliki Lila Koumandou
Agricultural University of Athens · Department of Biotechnology

PhD

About

65
Publications
7,943
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Introduction
Research Interests: Comparative genomics and evolution of diversity in biochemical systems - Bioenergetics: molecular evolution of diverse bioenergetic pathways in prokaryotes, bioenergetic diversity of the human gut microbiome - Endocellular trafficking: last eukaryotic common ancestor, prokaryote to eukaryote transition, biogenesis and cargo selection in bacterial outer membrane vesicles - Quorum sensing: comparative genomics and evolution of diverse systems, role in pathogenesis
Additional affiliations
March 2015 - March 2020
Agricultural University of Athens
Position
  • Lecturer
March 2013 - February 2015
Biomedical Research Foundation
Position
  • Marie Curie Research Fellow
December 2011 - February 2013
National and Kapodistrian University of Athens
Position
  • PostDoc Position
Education
October 2001 - September 2005
University of Cambridge
Field of study
  • Biochemistry
September 1993 - June 1997

Publications

Publications (65)
Article
Endomembrane system compartments are significant elements in virtually all eukaryotic cells, supporting functions including protein synthesis, post‐translational modifications and protein/lipid targeting. In terms of membrane area the endoplasmic reticulum (ER) is the largest intracellular organelle, but the origins of proteins defining the organel...
Article
Full-text available
Quorum sensing (QS) is a cell-to-cell communication system that enables bacteria to coordinate their gene expression depending on their population density, via the detection of small molecules called autoinducers. In this way bacteria can act collectively to initiate processes like bioluminescence, virulence and biofilm formation. Autoinducers are...
Article
Full-text available
Asperula naufraga is a rare and threatened obligate chasmophyte, endemic to Zakynthos island (Ionian islands, Greece). In this study, we provide a combined approach (including monitoring of demographic and reproductive parameters and study of genetic diversity) to assess the current conservation status of the species and to estimate its future exti...
Preprint
Full-text available
Quorum sensing (QS) is a cell-to-cell communication system that enables bacteria to coordinate their gene expression depending on their population density, via the detection of small molecules called autoinducers. In this way bacteria can act collectively to initiate processes like bioluminescence, virulence and biofilm formation. Autoinducers are...
Chapter
Pesticides are necessary to fight agricultural pests, yet they are often nonspecific, and their widespread use is a hazard to the environment and human health. The genomic era allows for new approaches to specifically target agricultural pests, based on analysis of their genome and their microbiome. We present such an approach, to combat Bactrocera...
Article
The human microbiome has lately emerged as an important factor in health and disease. The general patterns that emerge from metagenomics studies of the microbial diversity in the human gut of healthy adults, children and infants, are that (a) the microbiome is less diverse early in life, and gets enriched after infancy, and (b) that it is dominated...
Article
Full-text available
Prokaryotes use a wide variety of bioenergetic pathways but the order of emergence of these pathways and their evolutionary relationships are still unresolved issues. In this study we focus on the evolutionary relationships of different families of b-type cytochromes, which form part of a variety of bioenergetic enzymes (the cytochrome b6f complex,...
Article
Full-text available
Prokaryotes use a wide variety of bioenergetic pathways but the order of emergence of these pathways and their evolutionary relationships are still unresolved issues. In this study we focus on the evolutionary relationships of different families of b-type cytochromes, which form part of a variety of bioenergetic enzymes (the cytochrome b6f complex,...
Article
Full-text available
The Greek Goat Encephalitis virus (GGE) belongs to the Flaviviridae family of the genus Flavivirus. The GGE virus constitutes an important pathogen of livestock that infects the goat's central nervous system. The viral enzymes of GGE, helicase and RNA-dependent RNA polymerase (RdRP), are ideal targets for inhibitor design, since those enzymes are c...
Article
Full-text available
Bacteria and archaea are characterized by an amazing metabolic diversity, which allows them to persist in diverse and often extreme habitats. Apart from oxygenic photosynthesis and oxidative phosphorylation, well-studied processes from chloroplasts and mitochondria of plants and animals, prokaryotes utilize various chemo- or lithotrophic modes, suc...
Article
Full-text available
Members of the family Trypanosomatidae infect many organisms, including animals, plants and humans. Plant-infecting trypanosomes are grouped under the single genus Phytomonas, failing to reflect the wide biological and pathological diversity of these protists. While some Phytomonas spp. multiply in the latex of plants, or in fruit or seeds without...
Article
Gene fusion and fission events are important for evolutionary studies and for predicting protein-protein interactions. Previous studies have shown that fusion events always predominate over fission events and, in their majority, they represent singular events throughout evolution. In this project, the role of fusion and fission events in the genome...
Article
Full-text available
The Flaviviridae family of viruses infects vertebrates and is primarily spread through arthropod vectors. The Greek Goat Encephalitis (GGE) flavivirus belongs to the Flaviviridae family and specifically to the genus Flavivirus. GGE virus, which is endemic in Greece, is the causative agent of tick-borne encephalitis (TBE), an infection of the centra...
Article
Full-text available
Abstract Eukaryogenesis, the origin of the eukaryotic cell, represents one of the fundamental evolutionary transitions in the history of life on earth. This event, which is estimated to have occurred over one billion years ago, remains rather poorly understood. While some well-validated examples of fossil microbial eukaryotes for this time frame ha...
Article
Full-text available
The protozoan Trypanosoma brucei causes African Trypanosomiasis or sleeping sickness in humans, which can be lethal if untreated. Most available pharmacological treatments for the disease have severe side-effects. The purpose of this analysis was to detect novel protein-protein interactions (PPIs), vital for the parasite, which could lead to the de...
Data
Full-text available
The initial unique results found after the analysis performed using the SAFE software. Each code given below represents the GI number for each fused protein in each organism, according to the FASTA files used for the analysis, which are shown in Table 1. Codes highlighted in yellow are the fusion events that were successfully verified with backward...
Data
Full-text available
Fusion events detected in this study, for which no functional annotation is available. This table includes all the protein pairs that were found to participate in fusion events through the automated analysis using the SAFE software and verified by backward BLAST, and for which no functional annotation is available for either protein, i.e. both are...
Data
Full-text available
Fusion events detected in this study, for which functional annotation is available. This table includes all the protein pairs that were found to participate in fusion events through the automated analysis using the SAFE software and verified by backward BLAST, and for which functional annotation is available for both proteins. The results are group...
Data
Gene ontology (GO) annotation of the fusion events identified. The Uniprot gene ontology (GO) annotations (biological process, molecular function, cellular component), as well as the Conserved Domains Database (CDD) annotations, are shown for the 49 results that passed the backward BLAST verification; as some of the events were found multiple times...
Data
Phylogenetic trees on which the evolutionary categorization of the fusion events was based. These trees show the evolution of each protein pair throughout the tree of life. The highlighted oval shape indicates the species in which the fusion protein was identified. The colored dots along the tree branches represent the state of the protein in each...
Data
Full-text available
Available structural information for homologs of the domains which participate in the gene fusion events identified. For each of the 49 fusion events verified by reverse BLAST, the accession numbers of the corresponding protein pair in T. brucei is given. To identify available structural information, protein BLAST was used to compare each protein s...
Data
Fusion events detected in this study, for which only partial functional annotation is available. This table includes all the protein pairs that were found to participate in fusion events through the automated analysis using the SAFE software and verified by backward BLAST, and for which functional annotation is only available for one of the two pro...
Article
Full-text available
Kallikreins are secreted serine proteases with important roles in human physiology. Human plasma kallikrein, encoded by the KLKB1 gene on locus 4q34-35, functions in the blood coagulation pathway, and in regulating blood pressure. The human tissue kallikrein and kallikrein-related peptidases (KLKs) have diverse expression patterns and physiological...
Data
KLK gene clusters in selected species, as determined by examining the NCBI Gene database. The genetic locus neighborhood for KLKs in human, mouse, dog, cattle, opossum, chicken, lizard, and frog are shown. The KLK gene clusters in human, mouse, dog and cattle have a similar structure, except that dog is missing KLK3, cattle is missing KLK2 and KLK3...
Data
Masked alignment for the KLKs-all_human dataset. For each dataset, the alignment was produced using the program Muscle. Manual masking and trimming was performed in McClade. The files were then exported in Phylip3.6 simple text format. The accession numbers for all sequences can be found in Table S1, using the sequence name abbreviation given in th...
Data
Trimmed alignment for the KLKs-all_human dataset; the KLKs-all_human dataset was used to construct the tree shown in Figure 3. For each dataset, the alignment was produced using the program Muscle. Manual masking and trimming was performed in McClade. The files were then exported in Phylip3.6 simple text format. The accession numbers for all sequen...
Data
Multiple sequence alignment of human kallikreins with other serine proteases. All protein-coding alternative transcripts for each of the human tissue kallikreins, as well as plasma kallikrein, trypsin, chymotrypsin, plasminogen, and complement factor D were aligned using Muscle (also see Alignment S1). Conserved residues are highlighted in blue, an...
Data
Ensembl gene summaries showing the exon/intron boundaries for human, mouse and dog KLKs, which display significant structural variability. These transcript views form the basis of the data summarized in Figure 6. For all protein-coding isoforms shown, the numbers to the right indicate the order of coding exons, missed numbers indicate skipped exons...
Data
Phylogenetic reconstruction of all identified homologs of plasma and tissue kallikreins, from the 13 species studied, including all annotated protein-coding alternative transcripts. The tree shown is based on maximum likelihood analysis using PhyML. Similar results were obtained with RaxML, while MrBayes analysis with 3 million generations failed t...
Data
Accession numbers of all sequences used in this study. Refseq and ENSEMBL accession numbers are given for all annotated protein-coding transcripts of the sequences mentioned in the text. The gene name column lists the abbreviations used in the phylogenetic table and the multiple alignments. Transcript and exon supporting evidence from ENSEMBL is in...
Data
Masked alignment for the KLKs-one dataset. For each dataset, the alignment was produced using the program Muscle. Manual masking and trimming was performed in McClade. The files were then exported in Phylip3.6 simple text format. The accession numbers for all sequences can be found in Table S1, using the sequence name abbreviation given in the begi...
Data
Trimmed alignment for the KLKs-all dataset; the KLKs-all dataset was used to construct the tree shown in Figure S3. For each dataset, the alignment was produced using the program Muscle. Manual masking and trimming was performed in McClade. The files were then exported in Phylip3.6 simple text format. The accession numbers for all sequences can be...
Data
Masked alignment for the KLKs-all dataset. For each dataset, the alignment was produced using the program Muscle. Manual masking and trimming was performed in McClade. The files were then exported in Phylip3.6 simple text format. The accession numbers for all sequences can be found in Table S1, using the sequence name abbreviation given in the begi...
Data
Trimmed alignment for the KLKs-one dataset; the KLKs-one dataset was used to construct the tree shown in Figure 4. For each dataset, the alignment was produced using the program Muscle. Manual masking and trimming was performed in McClade. The files were then exported in Phylip3.6 simple text format. The accession numbers for all sequences can be f...
Data
The primary sequence of the NS3 domain of the Hepatitis C virus.
Data
Alignment of Hepacivirus NS3 protein sequences. The alignment was generated using Muscle, and visualized with Jalview. Amino acids are colored blue based on the Taylor color scheme (i.e. acidic/basic/polar).
Data
Alignment of Flaviviridae NS3 protein sequences. The alignment was generated using Muscle, and visualized with Jalview. Conserved residues are highlighted based on percent identity in the alignment (blue: >80% agreement, mid blue: >60% agreement, light blue: >40% agreement; only the residues that agree with the consensus residue for each column are...
Data
Details and accession numbers of all sequences used for the alignments and pylogenetic analysis. The table also indicates species names abbreviations used in Figs. 1, 2, S1, and S2.
Article
Full-text available
Viral RNA helicases are involved in duplex unwinding during the RNA replication of the virus. It is suggested that these helicases represent very promising antiviral targets. Viruses of the flaviviridae family are the causative agents of many common and devastating diseases, including hepatitis, yellow fever and dengue fever. As there is currently...
Article
Full-text available
Intracellular trafficking is a vital component of both virulence mechanisms and drug interactions in Trypanosoma brucei, the causative agent of human African trypanosomiasis and n'agana of cattle. Both maintaining the surface proteome composition within a life stage and remodeling the composition when progressing between life stages are important f...
Article
Full-text available
Domain Fusion Analysis takes advantage of the fact that certain proteins in a given proteome A, are found to have statistically significant similarity with two separate proteins in another proteome B. In other words, the result of a fusion event between two separate proteins in proteome B is a specific full-length protein in proteome A. In such a c...
Article
Full-text available
Domain or gene fusion analysis is a bioinformatics method for detecting gene fusions in one organism by comparing its genome to that of other organisms. The occurrence of gene fusions suggests that the two original genes that participated in the fusion are functionally linked, i.e. their gene products interact either as part of a multi-subunit prot...
Data
Full-text available
Alignments of the fused proteins identified in different species, with the corresponding split protein pairs in T. brucei. A: BLAST output alignment of the P. infestans EEY58132 composite protein with the T. brucei proteins AAX79027 and AAX70704. B: BLAST output alignment of the M. brevicollis EDQ88211 composite protein with the T. brucei proteins...
Data
Comparison of our results with those of Enright et al. [2]. To test the selectivity and performance of our automatic in-house software we used it to analyse the proteomes of the same organisms analysed by Enright et al. [2]. The table (Worksheet "COMPARISON") is based on supplementary table one of Enright et al. [2], showing "the 64 fusion events i...
Chapter
Eukaryotic cells depend on a complex network of intracellular organelles to perform endocytosis and exocytosis. These trafficking routes underlie many vital cellular processes, including nutrition, responses to environmental cues, defense from pathogens, and differentiation. Multiple disease mechanisms arise from defects in these pathways. How this...
Article
Full-text available
Intracellular trafficking and protein sorting are mediated by various protein complexes, with the retromer complex being primarily involved in retrograde traffic from the endosome or lysosome to the Golgi complex. Here, comparative genomics, cell biology and phylogenetics were used to probe the early evolution of retromer and its function. Retromer...
Data
Full-text available
Verification of phenotypes for VSG and CLH RNAi cell lines. Panel A: Growth curves of induced versus uninduced VSG RNAi cell lines, indicating growth arrest in the induced cell line over four days post induction. Panel B: CLH protein levels in induced (+Tet) versus uninduced (-Tet) CLH RNAi cell lines were examined by Western blotting. BiP was used...
Data
Significantly developmentally expressed trypanosome genes grouped by functional class. Numbers of transcripts on which the graph in Figure 2 is based. The number of genes for each functional class correspond to the ORFs featured in Table 1 and discussed in the text. Note that several of the oligonucleotides on the array target multicopy genes (e.g,...
Data
Full-text available
Response of T. brucei cells to dithiothreitol and tunicamycin treatment. Panel A: Growth curves for BSF cultures after the addition of dithiothreitol (DTT, 1–10 mM final concentrations) or tunicamycin (5–10 μg/ml final concentrations). Cell numbers diminish rapidly after the addition of DTT (within 4 hours), whereas cell growth is arrested after ad...
Article
Full-text available
Trypanosomatids utilise polycistronic transcription for production of the vast majority of protein-coding mRNAs, which operates in the absence of gene-specific promoters. Resolution of nascent transcripts by polyadenylation and trans-splicing, together with specific rates of mRNA turnover, serve to generate steady state transcript levels that can d...
Article
Turbulence has been shown to alter different aspects of the physiology of some dinoflagellates. The response appears to be species-specific and dependent on the experimental design and setup used to generate small-scale turbulence. We examined the variability of the response of three dinoflagellate species to the turbulence, following the same expe...
Article
Trypanosomes are members of the kinetoplastida, a group of divergent protozoan parasites responsible for considerable morbidity and mortality worldwide. These organisms have highly complex life cycles requiring modification of their cell surface together with engagement of immune evasion systems to effect survival; both processes intimately involve...
Data
Full-text available
Distribution of tethering complex subunits across representative eukaryotic taxa by BLAST. Data are based on BLAST results together with alignments – typically the S. cerevisiae or H. sapiens sequences were used as queries. Y = an identification based on a clear reverse BLAST result and/or additional evidence through analysis of the sequence by Clu...
Data
Full-text available
Coiled-coil domain annotations and regions of sequence similarity for selected tethering factors. Coiled-coil predictions were done using Coils, with default settings [65]. Regions of sequence similarity returned by PSI-BLAST are indicated by a grey bar for each prediction. Sequences are truncated at 800 residues for comparative purposes.
Data
Full-text available
Details of open reading frame selection, microarray oligonucleotides, qRT-PCR primers, database annotation and prior work. Functional groups assigned based on likely orthologs and/or domain annotation from multiple sources. Accession numbers are for T. brucei 927 at GeneDB, except ESAG6 and ESAG7 which are for T. brucei 427 at GeneDB, and VSG oligo...
Article
Full-text available
In membrane trafficking, the mechanisms ensuring vesicle fusion specificity remain to be fully elucidated. Early models proposed that specificity was encoded entirely by SNARE proteins; more recent models include contributions from Rab proteins, Syntaxin-binding (SM) proteins and tethering factors. Most information on membrane trafficking derives f...
Article
The chloroplast genome of algae and plants typically comprises a circular DNA molecule of 100-200kb, which harbours approximately 120 genes, and is present in 50-100 copies per chloroplast. However, in peridinin dinoflagellates, an ecologically important group of unicellular algae, the chloroplast genome is fragmented into plasmid-like 'minicircles...
Article
The chloroplast genome has a similar organization across a wide range of plants and algae. It comprises a circular molecule of >120 kb with >120 genes. However, the organization of chloroplast genes seems to be unique in dinoflagellate algae. In this ecologically important group of organisms, most of the chloroplast genes appear to have been lost,...
Article
Seven new minicircles, forming part of the fragmented plastid genome of the dinoflagellate Amphidinium operculatum, have been identified by PCR. Three minicircles are full-length, one of 2.6 kb encoding the 23S rRNA gene, one of 2.4 kb containing the psaB gene, and a third of 2.5 kb containing the psbD, psbE and psbI genes. This is the first report...
Article
Full-text available
We discuss the suggestion that differences in the nucleotide composition between plastid and nuclear genomes may provide a selective advantage in the transposition of genes from plastid to nucleus. We show that in the adenine, thymine (AT)-rich genome of Borrelia burgdorferi several genes have an AT-content lower than the average for the genome as...

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