Protein phosphorylation. Quality control of High-throughput phosphoproteomic data and statistical analysis.
Protein phosphorylation is the most abundant post-translational modification and a very attractive area of research for understanding biological complexity, cell regulation, for therapeutics, diagnostics and even for synthetic biology. By mutating phosphorylation sites (p-sites), molecular pathways and phenotypes may be manipulated. High-throughput (HTP) Phosphoproteomics has revolutionized this field, especially in the last five years. Despite the flood of these HTP data, there are concerns about their quality and about the level of biological noise in them. This project aims to address the issue of ‘noise’, provide highly curated and annotated datasets (in a database), use them for investigating the general properties, mechanisms and evolution of phosphorylation and develop relevant computational tools.
NAT/NCS2 nucleobase transporters
Nucleobase transporters are members of the APC superfamily of amino acid & nucleotide transporters (Saier et al, 2016) and are very important for the cells since their substrate uptake may function as nitrogen/carbon source, affect energy production, replication and protein synthesis through the salvage pathways for nucleotide synthesis (Papakostas et al, 2013; King et al, 2006). In addition to their important direct role on the central metabolism of the cell, they have been regarded as potentially important drug targets for viral/parasitic diseases, for cancer (Köse & Schiedel, 2009) or even mammalian physiology (sleep, drug and alcohol abuse, pain), since they regulate the levels of free nucleosides in circulation.
There exist 5 known families of transporters that use nucleobases as their main substrate, but the NAT/NCS2 family distinguishes from the others because it is very conserved and wide-spread across many different taxa (Frillingos, 2012).
Based on an evolutionary and bioinformatics analysis pipeline that we have already implemented in another superfamily, the tRNA synthetases – see (Chaliotis et al. 2017), we have generated a hierarchical evolutionary classification of the NAT/NCS2 family for prokaryotes. This classification helps to assign family members to evolutionary groups with distinct substrate preferences and identify key conserved and functional amino acids that affect substrate specificity.
Recombination in viral genomes.
Recombination along with point mutations are the main mechanisms of mutation contributing to virus evolution, especially in RNA viruses, such as HIV, Enteroviruses, Noroviruses etc. Although point mutations allow some investigation of the evolutionary fitness landscape, recombination leads to the virus to perform “jumps” within this evolutionary landscape and explore other regions. Furthermore, recombination has been identified as a mechanism of combining advantageous properties from various genomes into a new one, of eradicating deleterious mutations (i.e. act against Muller’s Ratchet), for development of drug resistance, or for evasion from the immune system. In addition, it has a disruptive effect on molecular phylogenetic analysis. Therefore, it is paramount to be able to detect such events and eventually correlate them with new properties or new outbreaks.
The rapid advances in sequencing technologies in combination with the small size of viral genomes is creating an explosion of genomic data in the public databases. Nevertheless, many of the current recombination tools are limited by the number of sequences being analyzed at one time. Therefore, there is a need for a new generation of tools that will rapidly scan hundreds or even thousands of genomes or sequence fragments and detect candidate recombination events that may later be further analyzed with more sensitive and specialized methods.Link to T-RECs Web Page
Link to Enterovirus Recombination Web Page
Evolution of the tRNA-synthetases superfamily.
Aminoacyl-tRNA synthetases (AARSs) mediate the accurate esterification of amino acids to their cognate tRNAs and thus represent an essential superfamily of enzymes responsible for the fidelity of the genetic code. Interestingly, gene duplication, divergence and gene loss are much more frequent events than originally considered. Paralogues or even paralogue fragments of AARSs exhibit diverse functions outside translation, spanning from editing and antibiotic resistance in bacteria to molecular hubs within essential signaling pathways that regulate tumorigenesis in human. Our work focuses on developing new computational skills for identifying these synthetases in proteomes, on storing the data in a database scheme and on analyzing data from thousands of prokaryotic genomes in order to understand what drives the evolution and diversity of this superfamily.Link to web application
Evolution of gene regulation with a special interest on protein interaction networks and dimerization of transcription factors (bZIP, bHLH, Nuclear Receptors).
In many eukaryotic transcription factor gene families, proteins require a physical interaction with an identical molecule or with another molecule within the same family to form a functional dimer and bind DNA. Depending on the choice of partner and the cellular context, each dimer triggers a sequence of regulatory events that lead to a particular cellular fate, for example, proliferation or differentiation. Recent syntheses of genomic and functional data reveal that partner choice is not random; instead, dimerization specificities, which are strongly linked to the evolution of the protein family, apply. Our focus is on understanding these interaction specificities, their functional consequences and how they evolved. This knowledge is essential for understanding gene regulation and designing a new generation of drugs.
Research Grants awarded
Filtering, Annotation and Bioinformatics analyses of high-throughput Phosphoproteomic data (FAB-PHOS). Principal Investigator: GD Amoutzias. Funded by Aristeia II - GSRT.
Bioinformatic analysis of human genomic and phosphoproteomic data. Principal Investigator: GD Amoutzias. Funded by The Research Committee of the University of Thessaly.
Due to the interdisciplinary nature of Bioinformatics, the lab has a series of ongoing collaborations with experimental as well as in-silico labs such as:
Prof. Markoulatos and Dr. Mosialos, Laboratory of Virology and Bacteriology, Dept. Biochemistry and Biotechnology, University of Thessaly, Greece.
Prof. Van de Peer, Bioinformatics and Genomics Laboratory, Dept. of Plant Systems Biology, VIB/UGent, Belgium.
Prof. Robertson, Viral Genomics and Bioinformatics Laboratory, Centre for Virus Research, Institute of Infection, Immunity and Inflammation, University of Glasgow, UK.
Prof. Oliver, Yeast Systems Biology laboratory, Dept. of Biochemistry, Cambridge University, UK.
Prof. Frillingos, School of Medicine, University of Ioannina, Greece.
Assist. Prof. Papanikolaou, School of Medicine, Aristotle University of Thessaloniki, Greece.
Prof. Stathopoulos, Laboratory of Biochemistry, School of Medicine, University of Patra, Greece.
Prof. Katis and Dr. Maliogka, Laboratory of Plant Pathology, School of Agriculture, Aristotle University of Thessaloniki, Greece
Dr. Stratikos, Demokritos Research Center, Athens Greece.
Invited speakers by the Laboratory of Bioinformatics:
- 05/04.2017: Prof Efstathios Frillingos, School of Medicine, University of Ioannina, Greece. Relatioships between structure, function and substrate specificity of nucleobase transporters.
- 15/6/2016: Prof. Steve Oliver, Dept. of Biochemistry, University of Cambridge, UK. Computational models for Synthetic Biology.
- 3/6/2015: Dr. Liana Tsiatsiani, Utrecht University, Netherlands. Proteolytic enzymes and shotgun proteomics: a win-win situation.
- 20/5/2015: Dr. Eva Fernandez, Research Centre in Evolutionary Anthropology and Paleoecology, Liverpool John Moores University, UK. Ancient human DNA from the Fertile Crescent: reconstructing the primary routes of the Neolithic expansion into Europe.
- 22/4/2015: Dr. Stratos Stratikos, Demokritos Research Center, Athens, Greece. Intracellular antigen processing as a node of adaptive immune response regulation.
- 18/3/2015. Dr. Ioannis Iliopoulos, Dept of Medicine, University of Crete, Greece. Protein Association Discovery in Biomedical Literature.
- 4/4/2012: Prof. Steve Oliver, Dept. of Biochemistry, University of Cambridge. Systems Biology: A science in flux.
- Prof. Steve Oliver, Dept. of Biochemistry, University of Cambridge, UK. Sabbatical visit. 6 - 17 June 2016
46) Ntountoumi C, Fliatoura V, Vlastaridis P, Iliopoulos I, Oliver SG, Papanikolaou NA, Amoutzias GD. Methyl-Prometheus: A Neural Network webserver for proteome-scale prediction of eukaryotic Arginine/Lysine methylation sites. Under Revision in Proteomics.
45) Chaliotis A, Vlastaridis P, Ntountoumi, C, Botou M, Yalelis V, Lazou P, Tatsaki E, Mossialos D, Frillingos S* and Amoutzias GD. NAT/NCS2-hound: A webserver for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase-cation symporters of the NAT/NCS2 family. Under revision in Gigascience.
44) Nikolaidis M, Mimouli K, Kyriakopoulou Z, Tsimpidis M, Tsakogiannis D, Markoulatos P, Amoutzias GD. Large-scale genomic analysis reveals recurrent patterns of intertypic recombination in human enteroviruses. Under revision in Virology.
43) Karakasidou K, Nikolouli K, Amoutzias GD, Pournou A, Manassis C, Tsiamis G,Mossialos D. Microbial diversity in biodeteriorated Greek historical documents dating back to the 19th and 20th century: A case study. In press, Microbiology Open, 2018. DOI: 10.1002/mbo3.596
42) Priftis A, Goutzourelas N, Chalabalaki M, Ntasi G, Stagos D, Amoutzias GD, Skaltsounis LA, Kouretas D. Effect of polyphenols from coffee and grape on gene expression in myoblasts. Mech Ageing Dev. 2017 Nov 23. pii: S0047-6374(17)30155-0. doi: 10.1016/j.mad.2017.11.015.
41) Tsakogiannis D, Moschonas GD, Bella E, Kyriakopoulou Z, Amoutzias GD, Dimitriou TG, Kottaridi C, Markoulatos P. Association of p16 (CDKN2A) polymorphisms with the development of HPV16-related precancerous lesions and cervical cancer in the Greek population. J Med Virol. 2017 Nov 23. doi: 10.1002/jmv.24996.
40) Kyriakopoulou Z, Amoutzias GD, Dimitriou TG, Tsakogiannis D, Mossialos D, Markoulatos P. Intra- and inter-serotypic recombinations in the 5΄ UTR-VP4 region of Echovirus 30 strains. Arch Virol. 2017 Oct 30. doi: 10.1007/s00705-017-3600-1.
39) Fikatas A, Dimitriou TG, Kyriakopoulou Z, Moschonas GD, Amoutzias GD, Mossialos D, Gartzonika C, Levidiotou-Stefanou S, Markoulatos P. Detection of negative and positive RNA strand of poliovirus Sabin 1 and echovirus E19 by a stem-loop reverse transcription PCR. Lett Appl Microbiol. 2017 Jun 20. doi: 10.1111/lam.12766. PMID: 28631392
38) Vlastaridis P, Kyriakidou P, Chaliotis A, Van de Peer Y, Oliver SG, Amoutzias GD. Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes. Gigascience. 2017 Feb 1;6(2):1-11. doi: 10.1093/gigascience/giw015. PMID:28327990
37) Vlastaridis P., Papakyriakou A., Chaliotis A., Stratikos E., Oliver SG. and Amoutzias GD. The pivotal role of protein phosphorylation in the control of yeast central metabolism. G3: Genes, Genomes, Genetics 2017 Mar 1. pii: g3.116.037218. PMID: 28250014
36) Tsimpidis M, Bachoumis G, Mimouli K, Kuriakopoulou Z, Robertson DL, Markoulatos P, Amoutzias GD.T-RECs: Rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes. BMC Bioinformatics. 2017 Jan 5;18(1):13. PMID:28056784
35) Chaliotis A, Vlastaridis P, Mossialos D, Ibba M, Becker HD, Stathopoulos C and Amoutzias GD. The complex evolutionary history of aminoacyl-tRNA synthetases. Nucleic Acids Res. 2017 Feb 17;45(3):1059-1068. PMID: 28180287
34) Fikatas A, Dimitriou TG, Kyriakopoulou Z, Tsachouridou O, Gartzonika C, Levidiotou-Stefanou S, Amoutzias GD, Markoulatos P. Serum neutralization assay for the determination of antibody levels against non-polio enterovirus strains in Central and Western Greece. Viral Immunol. 2016 Sep;29(7):444-50. PMID: 27410516
33) Amoutzias GD, Giannoulis T, Moutou KA, Psarra AG, Stamatis C, Tsipourlianos A, Mamuris Z. SNP identification through transcriptome analysis of the European brown hare (Lepus europaeus): cellular energetics and mother’s curse. PLoS One. 2016 Jul 26;11(7). PMID: 27459096
32) Vlastaridis P, Oliver SG, Van de Peer Y, Amoutzias GD. The Challenges of Interpreting Phosphoproteomics Data: A Critical View Through the Bioinformatics Lens. Lecture Notes in Bioinformatics. 2016. 9874, pp. 196-204.
31) Amoutzias GD, Chaliotis A, Mossialos D. Discovery Strategies of Bioactive Compounds Synthesized by Nonribosomal Peptide Synthetases and Type-I Polyketide Synthases Derived from Marine Microbiomes. Mar Drugs. 2016 Apr 16;14(4). pii: E80. PMID: 27092515
30) Pappi PG, Maliogka VI, Amoutzias GD, Katis NI. Genetic variation of eggplant mottled dwarf virus from annual and perennial plant hosts. Arch Virol. 2016 Mar;161(3):631-9. PMID: 26660163
29) Katsiani, A.T., Maliogka, V.I., Amoutzias, GD, Efthimiou, K.E., Katis, N.I. Insights into the genetic diversity and evolution of Little cherry virus 1. Plant Pathology 2015, 64 (4), pp. 817-824. DOI: 10.1111/ppa.12309
28) Kyriakopoulou Z, Bletsa M, Tsakogiannis D, Dimitriou TG, Amoutzias GD, Gartzonika C, Levidiotou-Stefanou S, Markoulatos P. Molecular epidemiology and evolutionary dynamics of Echovirus 3 serotype. Infect Genet Evol. 2015 Jun;32:305-12. PMID: 25791929
27) Kyriakopoulou Z, Pliaka V, Amoutzias GD, Markoulatos P. Recombination among human non-polio enteroviruses: implications for epidemiology and evolution. Virus Genes. 2015 Apr;50(2):177-88 PMID: 25537948
26) Tsakogiannis D, Kyriakopoulou Z, Ruether IG, Amoutzias GD, Dimitriou TG, Diamantidou V, Kotsovassilis C, Markoulatos P. Determination of HPV16 physical status through E1/E6 and E2/E6 ratio analysis. J Med Microbiol. 2014 Sep 11. pii: jmm.0.076810-0. PMID: 25212758
25) Ruether IG, Dimitriou TG, Tsakogiannis D, Kyriakopoulou Z, Amoutzias GD, Gartzonika C, Levidiotou-Stefanou S, Markoulatos P. Characterization of novel intergenogroup and intergenotype recombinant noroviruses from central Greece. Mol Cell Probes. 2014 Aug;28(4):204-10. PMID: 24751495
24) Tsakogiannis D, Darmis F, Gortsilas P, Ruether IG, Kyriakopoulou Z, Dimitriou TG, Amoutzias G, Markoulatos P. Nucleotide polymorphisms of the human papillomavirus 16 E1 gene. Arch Virol. 2014 Jan;159(1):51-63. PMID: 23881083
23) Tsakogiannis D, Kyriakopoulou Z, Amoutzias G, Ruether IG, Dimitriou TG, Panotopoulou E, Markoulatos P. Identification of novel E6-E7 sequence variants of human papillomavirus 16. Arch Virol. 2013 Apr;158(4):821-8. PMID: 23208280
22) Stagos D, Amoutzias GD, Matakos A, Spyrou A, Tsatsakis AM, Kouretas D. Chemoprevention of liver cancer by plant polyphenols. Food Chem Toxicol. 2012 Jun;50(6):2155-70. PMID: 22521445
21) Cock MJ, Sterck L, Rouzé P, Scornet D, Allen AE, Amoutzias G, et al. The Ectocarpus Genome and Brown Algal Genomics. The Ectocarpus Genome Consortium. Advances in Botanical Research. 2012. Volume 64, 2012, Pages 141-184. DOI: 10.1016/B978-0-12-391499-6.00005-0
20) Amoutzias GD, He Y, Lilley KS, Van de Peer Y, Oliver SG. Evaluation and properties of the budding yeast phosphoproteome. Mol Cell Proteomics. 2012 Jun;11(6):M111.009555. PMID: 22286756
19) Cock MJ, Sterck L, Rouzé P, Scornet D, Allen AE, Amoutzias G, et al. The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature. 2010 Jun 3;465(7298):617-21. PMID: 20520714
18) Amoutzias GD, He Y, Gordon J, Mossialos D, Oliver SG, Van de Peer Y. Posttranslational regulation impacts the fate of duplicated genes. Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):2967-71. PMID: 20080574
17) Mossialos D, Amoutzias GD. Role of siderophores in cystic fibrosis (CF) pathogenesis: foes or friends? Int J Med Microbiol. 2009 Feb;299(2):87-98. PMID: 18755629
16) Amoutzias GD, Robertson DL, Van de Peer Y, Oliver SG. Choose your partners: Dimerization in eukaryotic transcription factors. Trends Biochem Sci. 2008 May;33(5):220-9. PMID: 18406148
15) Amoutzias GD, Van de Peer Y, Mossialos D. Evolution and taxonomic distribution of non-ribosomal peptide and polyketide synthases. Future Microbiol. 2008 Jun;3:361-70. PMID: 18505401
14) Amoutzias G, Van de Peer Y. Together we stand: genes cluster to coordinate regulation. Dev Cell. 2008 May;14(5):640-2. PMID: 18477446
13) Pinney JW, Amoutzias GD, Rattray M, Robertson DL. Reconstruction of ancestral protein interaction networks for the bZIP transcription factors. Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20449-53. PMID: 18077348
12) Pampalakis G, Arampatzidou M, Amoutzias G, Kossida S, Sotiropoulou G. Identification and analysis of mammalian KLK6 orthologue genes for prediction of physiological substrates. Comput Biol Chem. 2007 Nov 29. PMID: 18243805
11) Mossialos D, Amoutzias G. Siderophores in fluorescent pseudomonads: new tricks from an old dog. Future Microbiol. 2007 Aug;2:387-95. PMID: 17683275
10) Amoutzias GD, Pichler EE, Mian N, De Graaf D, Imsiridou A, Robinson-Rechavi M, Bornberg-Bauer E, Robertson DL, Oliver SG. A protein interaction atlas for the nuclear receptors: Properties and quality of a hub-based dimerisation network. BMC Syst Biol. 2007 Jul 31;1(1):34. PMID: 17672894
9) Holden BJ, Pinney JW, Lovell SC, Amoutzias GD & Robertson DL. An exploration of alternative visualizations of the basic helix-loop-helix protein interaction network. BMC Bioinformatics. 2007 Aug 6;8(1):289. PMID: 17683601
8) Amoutzias G, Veron A, Weiner A, Robinson-Rechavi M, Bornberg-Bauer E, Oliver S, Robertson D. One Billion Years of bZIP Transcription Factor Evolution: Conservation and Change in Dimerization, and DNA-Binding Site Specificity. Mol Biol Evol. 2006 Dec 28. PMID: 17194801
7) Amoutzias GD, Bornberg-Bauer E, Oliver SG, Robertson DL. The Reduction/oxidation-phosphorylation control of the DNA binding of the bZIP family is linked with its dimerization network. BMC Genomics 2006 May 4;7:107. PMID:
6) Podowski RM, Cleary JG, Goncharoff NT, Amoutzias G, Hayes WS. Suregene, a scalable system for automated term disambiguation of gene and protein names. J Bioinform Comput Biol. 2005 Jun;3(3):743-70. PMID: 16108092
5) Amoutzias GD, Weiner J, Bornberg-Bauer E. Phylogenetic profiling of protein interaction networks in eukaryotic transcription factors reveals focal proteins being ancestral to hubs. Gene. 2005 Feb 23. PMID: 15777629
4) Amoutzias GD, Robertson DL, Oliver SG, Bornberg-Bauer E. Convergent evolution of gene networks by single-gene duplications in higher eukaryotes.. EMBO Rep. 2004 Mar;5(3):274-9. PMID: 14968135
3) Amoutzias GD, Robertson DL, Bornberg-Bauer E. The evolution of protein interaction networks in regulatory proteins. Comp Funct Genomics 2004; 5: 79-84. PMID: 18629034
2) Podowski RM, Cleary JG, Goncharoff NT, Amoutzias G, Hayes WS. AZuRE, a scalable system for automated term disambiguation of gene and protein names. Proc IEEE Comput Syst Bioinform Conf. 2004;:415-24. PMID: 16448034
1) Imsiridou A, Hardy H, Maudling N, Amoutzias G, Zaldivar Comenges JM. Web database of molecular genetic data from fish stocks. J Hered. 2003 May-Jun;94(3):265-7. PMID: 12816969