Imperial College London

DrIolyKotta-Loizou

Faculty of Natural SciencesDepartment of Life Sciences

Research Associate
 
 
 
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i.kotta-loizou13

 
 
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Sir Alexander Fleming BuildingSouth Kensington Campus

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Publications

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55 results found

Kotta-Loizou I, Giuliano MG, Jovanovic M, Schaefer J, Ye F, Zhang N, Irakleidi DA, Liu X, Zhang X, Buck M, Engl Cet al., 2022, The RNA repair proteins RtcAB regulate transcription activator RtcR via its CRISPR-associated Rossmann fold domain., iScience, Vol: 25

CRISPR-associated Rossmann fold (CARF) domain signaling underpins modulation of CRISPR-Cas nucleases; however, the RtcR CARF domain controls expression of two conserved RNA repair enzymes, cyclase RtcA and ligase RtcB. Here, we demonstrate that RtcAB are required for RtcR-dependent transcription activation and directly bind to RtcR CARF. RtcAB catalytic activity is not required for complex formation with CARF, but is essential yet not sufficient for RtcRAB-dependent transcription activation, implying the need for an additional RNA repair-dependent activating signal. This signal differs from oligoadenylates, a known ligand of CARF domains, and instead appears to originate from the translation apparatus: RtcB repairs a tmRNA that rescues stalled ribosomes and increases translation elongation speed. Taken together, our data provide evidence for an expanded range for CARF domain signaling, including the first evidence of its control via in trans protein-protein interactions, and a feed-forward mechanism to regulate RNA repair required for a functioning translation apparatus.

Journal article

Kotta-Loizou I, 2022, Molecular origins of transcriptional heterogeneity in diazotrophic Klebsiella oxytoca, mSystems, Vol: 7, Pages: 1-13, ISSN: 2379-5077

Phenotypic heterogeneity in clonal bacterial batch cultures has been shown for a range of bacterial systems; however, the molecular origins of such heterogeneity and its magnitude are not well understood. Under conditions of extreme low-nitrogen stress in the model diazotroph Klebsiella oxytoca, we found remarkably high heterogeneity of nifHDK gene expression, which codes for the structural genes of nitrogenase, one key enzyme of the global nitrogen cycle. This heterogeneity limited the bulk observed nitrogen-fixing capacity of the population. Using dual-probe, single-cell RNA fluorescent in situ hybridization, we correlated nifHDK expression with that of nifLA and glnK-amtB, which code for the main upstream regulatory components. Through stochastic transcription models and mutual information analysis, we revealed likely molecular origins for heterogeneity in nitrogenase expression. In the wild type and regulatory variants, we found that nifHDK transcription was inherently bursty, but we established that noise propagation through signaling was also significant. The regulatory gene glnK had the highest discernible effect on nifHDK variance, while noise from factors outside the regulatory pathway were negligible. Understanding the basis of inherent heterogeneity of nitrogenase expression and its origins can inform biotechnology strategies seeking to enhance biological nitrogen fixation. Finally, we speculate on potential benefits of diazotrophic heterogeneity in natural soil environments.

Journal article

Patil RH, Kotta-Loizou I, Palyzová A, Pluháček T, Coutts RHA, Stevens DA, Havlíček Vet al., 2022, Correction: Patil et al. Freeing Aspergillus fumigatus of Polymycovirus Infection Renders It More Resistant to Competition with Pseudomonas aeruginosa Due to Altered Iron-Acquiring Tactics. J. Fungi 2021, 7, 497, Journal of Fungi, Vol: 8, ISSN: 2309-608X

In the original publication [...].

Journal article

Kotta-Loizou I, Coutts RHA, Ictv Report Consortium, 2022, ICTV virus taxonomy profile: polymycoviridae 2022., Journal of General Virology, Vol: 103, Pages: 1-2, ISSN: 0022-1317

Members of the family Polymycoviridae are small viruses with multi-segmented and non-conventionally encapsidated double-stranded (ds) RNA genomes. Typically, polymycoviruses have four genomic segments, although some have up to eight. The genus Polymycovirus includes several species whose members infect fungi (ascomycetes and basidiomycetes), and oomycetes, altering host morphology, sporulation, growth and virulence. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Polymycoviridae, which is available at ictv.global/report/polymycoviridae.

Journal article

Fu M, Zhang H, Yin M, Han Z, Bai Q, Peng Y, Shafik K, Zhai L, Hong N, Xu W, Wang G, Kotta-Loizou Iet al., 2022, A novel heptasegmented positive-sense single-stranded RNA virus from the phytopathogenic fungus colletotrichum fructicola, Journal of Virology, Vol: 96, Pages: 1-14, ISSN: 0022-538X

In this study, a novel positive-sense single-stranded RNA (+ssRNA) mycovirus, tentatively named Colletotrichum fructicola RNA virus 1 (CfRV1), was identified in the phytopathogenic fungus Colletotrichum fructicola. CfRV1 has seven genomic components, encoding seven proteins from open reading frames (ORFs) flanked by highly conserved untranslated regions (UTRs). Proteins encoded by ORFs 1, 2, 3, 5, and 6 are more similar to the putative RNA-dependent RNA polymerase (RdRp), hypothetical protein (P2), methyltransferase, and two hypothetical proteins of Hadaka virus 1 (HadV1), a capsidless 10- or 11-segmented +ssRNA virus, while proteins encoded by ORFs 4 and 7 showed no detectable similarity to any known proteins. Notably, proteins encoded by ORFs 1 to 3 also share considerably high similarity with the corresponding proteins of polymycoviruses. Phylogenetic analysis conducted based on the amino acid sequence of CfRV1 RdRp and related viruses placed CfRV1 and HadV1 together in the same clade, close to polymycoviruses and astroviruses. CfRV1-infected C. fructicola strains demonstrate a moderately attenuated growth rate and virulence compared to uninfected isolates. CfRV1 is capsidless and potentially encapsulated in vesicles inside fungal cells, as revealed by transmission electron microscopy. CfRV1 and HadV1 are +ssRNA mycoviruses closely related to polymycoviruses and astroviruses, represent a new linkage between +ssRNA viruses and the intermediate double-stranded RNA (dsRNA) polymycoviruses, and expand our understanding of virus diversity, taxonomy, evolution, and biological traits. IMPORTANCE A scenario proposing that dsRNA viruses evolved from +ssRNA viruses is still considered controversial due to intergroup knowledge gaps in virus diversity. Recently, polymycoviruses and hadakaviruses were found as intermediate dsRNA and +ssRNA stages, respectively, between +ssRNA and dsRNA viruses. Here, we identified a novel +ssRNA mycovirus, Colletotrichum fructicola RNA virus

Journal article

Hao M, Ye F, Jovanovic M, Kotta-Loizou I, Xu Q, Qin X, Buck M, Zhang X, Wang Met al., 2022, Structures of Class I and Class II transcription complexes reveal the molecular basis of RamA-dependent transcription activation, Advanced Science, Vol: 9, Pages: 1-10, ISSN: 2198-3844

Transcription activator RamA is linked to multidrug resistance of Klebsiella pneumoniae through controlling genes that encode efflux pumps (acrA) and porin-regulating antisense RNA (micF). In bacteria, σ70, together with activators, controls the majority of genes by recruiting RNA polymerase (RNAP) to the promoter regions. RNAP and σ70 form a holoenzyme that recognizes -35 and -10 promoter DNA consensus sites. Many activators bind upstream from the holoenzyme and can be broadly divided into two classes. RamA acts as a class I activator on acrA and class II activator on micF, respectively. The authors present biochemical and structural data on RamA in complex with RNAP-σ70 at the two promoters and the data reveal the molecular basis for how RamA assembles and interacts with core RNAP and activates transcription that contributes to antibiotic resistance. Further, comparing with CAP/TAP complexes reveals common and activator-specific features in activator binding and uncovers distinct roles of the two C-terminal domains of RNAP α subunit.

Journal article

Moriyama H, Kotta-Loizou I, Kim K-H, Xie Jet al., 2021, Editorial: Mycoviruses and related viruses infecting fungi, lower eukaryotes, plants and insects, Frontiers in Microbiology, Vol: 12, ISSN: 1664-302X

Journal article

Wu C-F, Aoki N, Takeshita N, Fukuhara T, Chiura HX, Arie T, Kotta-Loizou I, Okada R, Komatsu K, Moriyama Het al., 2021, Unique terminal regions and specific deletions of the segmented double-stranded RNA genome of Alternaria alternata virus 1, in the proposed family Alternaviridae, Frontiers in Microbiology, Vol: 12, ISSN: 1664-302X

Alternaria alternata virus 1 (AaV1) has been identified in the saprophytic fungus Alternaria alternata strain EGS 35-193. AaV1 has four genomic double-stranded (ds)RNA segments (dsRNA1-4) packaged in isometric particles. The 3' end of each coding strand is polyadenylated (36-50nt), but the presence of a cap structure at each 5' end has not previously been investigated. Here, we have characterized the AaV1 genome and found that it has unique features among the mycoviruses. We confirmed the existence of cap structures on the 5' ends of the AaV1 genomic dsRNAs using RNA dot blots with anti-cap antibodies and the oligo-capping method. Polyclonal antibodies against purified AaV1 particles specifically bound to an 82kDa protein, suggesting that this protein is the major capsid component. Subsequent Edman degradation indicated that the AaV1 dsRNA3 segment encodes the major coat protein. Two kinds of defective AaV1 dsRNA2, which is 2,794bp (844 aa) in length when intact, appeared in EGS 35-193 during subculturing, as confirmed by RT-PCR and northern hybridization. Sequence analysis revealed that one of the two defective dsRNA2s contained a 231bp deletion, while the other carried both the 231bp deletion and an additional 465bp deletion in the open reading frame. Both deletions occurred in-frame, resulting in predicted proteins of 767 aa and 612 aa. The fungal isolates carrying virions with the defective dsRNA2s showed impaired growth and abnormal pigmentation. To our best knowledge, AaV1 is the first dsRNA virus to be identified with both 5' cap and 3'poly(A) structures on its genomic segments, as well as the specific deletions of dsRNA2.

Journal article

Kotta-Loizou I, 2021, Mycoviruses and their role in fungal pathogenesis, CURRENT OPINION IN MICROBIOLOGY, Vol: 63, Pages: 10-18, ISSN: 1369-5274

Journal article

Waite C, Lindstrom-Battle A, Bennett M, Carey M, Kotta-Loizou I, Hong C, Buck M, Schumacher Jet al., 2021, Resource allocation during the transition to diazotrophy in Klebsiella oxytoca, Frontiers in Microbiology, Vol: 12, Pages: 1-20, ISSN: 1664-302X

Free-living nitrogen-fixing bacteria can improve growth yields of some non-leguminous plants and, if enhanced through bioengineering approaches, have the potential to address major nutrient imbalances in global crop production by supplementing inorganic nitrogen fertilizers. However, nitrogen fixation is a highly resource-costly adaptation and is de-repressed only in environments in which sources of reduced nitrogen are scarce. Here we investigate nitrogen fixation (nif) gene expression and nitrogen starvation response signalling in the model diazotroph Klebsiella oxytoca (Ko) M5a1 during ammonium depletion and the transition to growth on atmospheric N2. Exploratory RNA-sequencing revealed that over 50% of genes were differentially expressed under diazotrophic conditions, among which the nif genes are among the most highly expressed and highly upregulated. Isotopically labelled QconCAT standards were designed for multiplexed, absolute quantification of Nif and nitrogen-stress proteins via multiple reaction monitoring mass spectrometry (MRM-MS). Time-resolved Nif protein concentrations were indicative of bifurcation in the accumulation rates of nitrogenase subunits (NifHDK) and accessory proteins. We estimate that the nitrogenase may account for more than 40% of cell protein during diazotrophic growth and occupy approximately half the active ribosome complement. The concentrations of free amino acids in nitrogen-starved cells were insufficient to support the observed rates of Nif protein expression. Total Nif protein accumulation was reduced 10-fold when the NifK protein was truncated and nitrogenase catalysis lost (nifK1-1203), implying that reinvestment of de novo fixed nitrogen is essential for further nif expression and a complete diazotrophy transition. Several amino acids accumulated in non-fixing ΔnifLA and nifK1-1203 mutants, while the rest remained highly stable despite prolonged N starvation. Monitoring post-translational uridylylation of the PII-type

Journal article

Zhou L, Li X, Kotta-Loizou I, Dong K, Li S, Ni D, Hong N, Wang G, Xu Wet al., 2021, A mycovirus modulates the endophytic and pathogenic traits of a plant associated fungus, The ISME Journal: multidisciplinary journal of microbial ecology, Vol: 15, Pages: 1893-1906, ISSN: 1751-7362

Fungi are generally thought to live in host plants with a single lifestyle, being parasitism, commensalism, or mutualism. The former, known as phytopathogenic fungi, cause various plant diseases that result in significant losses every year; while the latter, such as endophytic fungi, can confer fitness to the host plants. It is unclear whether biological factors can modulate the parasitic and mutualistic traits of a fungus. In this study, we isolated and characterized a mycovirus from an endophytic strain of the fungus Pestalotiopsis theae, a pathogen of tea (Camellia sinensis). Based on molecular analysis, we tentatively designated the mycovirus as Pestalotiopsis theae chrysovirus-1 (PtCV1), a novel member of the family Chrysoviridae, genus Alphachrysovirus. PtCV1 has four double-stranded (ds) RNAs as its genome, ranging from 0.9 to 3.4 kbp in size, encapsidated in isometric particles. PtCV1 significantly reduced the growth rates of its host fungus in vitro (ANOVA; P-value < 0.001) and abolished its virulence in planta (ANOVA; P-value < 0.001), converting its host fungus to a non-pathogenic endophyte on tea leaves, while PtCV1-free isolates were highly virulent. Moreover, the presence of PtCV1 conferred high resistance to the host plants against the virulent P. theae strains. Here we report a mycovirus that modulates endophytic and phytopathogenic fungal traits and provides an alternative approach to biological control of plant diseases caused by fungi.

Journal article

Patil RH, Kotta-Loizou I, Palyzová A, Pluháček T, Coutts RHA, Stevens DA, Havlíček Vet al., 2021, Freeing Aspergillus fumigatus of polymycovirus infection renders it more resistant to competition with pseudomonas aeruginosa due to altered iron-acquiring tactics, Journal of Fungi, Vol: 7, ISSN: 2309-608X

A virus-free (VF) A. fumigatus isolate has been shown to be resistant in competition with Pseudomonas as compared to the isogenic line infected with Aspergillus fumigatus polymycovirus 1 (AfuPmV-1), and this phenotype was apparently related to alterations in iron metabolism. Here we investigated further the mechanisms underpinning this phenotype. The extracellular siderophore profiles of five isogenic VF and virus-infected (VI) strains were sampled at 24, 31, 48, 54, and 72 h in submerged cultures and quantitatively examined by liquid chromatography and mass spectrometry. Intracellular profiles of conidia and cultures at the stationary growth phase were defined. VF A. fumigatus demonstrated the best fitness represented by the fastest onset of its exponential growth when grown on an iron-limited mineral medium. The exponential phase and transitional production phase of the extracellular triacetylfusarinine C (TafC) were achieved at 24 and 31 h, respectively, contrary to VI strains, which acted more slowly. As a result, the TafC reservoir was consumed sooner in the VF strain. Additionally, the VF strain had lower ferricrocin and higher hydroxyferricrocin content in the pellet during the stationary phase. All of these differences were significant (Kruskal-Wallis, p < 0.01). In our study, the siderophore reservoir of a VF strain was consumed sooner, improving the fitness of the VF strain in competition with P. aeruginosa.

Journal article

Abdoulaye AH, Hai D, Tang Q, Jiang D, Fu Y, Cheng J, Lin Y, Li B, Kotta-Loizou I, Xie Jet al., 2021, Two distant helicases in one mycovirus: evidence of horizontal gene transfer between mycoviruses, coronaviruses and other nidoviruses, VIRUS EVOLUTION, Vol: 7

Journal article

Nazik H, Kotta-Loizou I, Sass G, Coutts RHA, Stevens DAet al., 2021, Virus infection of Aspergillus fumigatus compromises the fungus in intermicrobial competition, Viruses-Basel, Vol: 13, ISSN: 1999-4915

Aspergillus and Pseudomonas compete in nature, and are the commonest bacterial and fungal pathogens in some clinical settings, such as the cystic fibrosis lung. Virus infections of fungi occur naturally. Effects on fungal physiology need delineation. A common reference Aspergillus fumigatus strain, long studied in two (of many) laboratories, was found infected with the AfuPmV-1 virus. One isolate was cured of virus, producing a virus-free strain. Virus from the infected strain was purified and used to re-infect three subcultures of the virus-free fungus, producing six fungal strains, otherwise isogenic. They were studied in intermicrobial competition with Pseudomonasaeruginosa. Pseudomonas culture filtrates inhibited forming or preformed Aspergillus biofilm from infected strains to a greater extent, also seen when Pseudomonas volatiles were assayed on Aspergillus. Purified iron-chelating Pseudomonas molecules, known inhibitors of Aspergillus biofilm, reproduced these differences. Iron, a stimulus of Aspergillus, enhanced the virus-free fungus, compared to infected. All infected fungal strains behaved similarly in assays. We show an important consequence of virus infection, a weakening in intermicrobial competition. Viral infection may affect the outcome of bacterial–fungal competition in nature and patients. We suggest that this occurs via alteration in fungal stress responses, the mechanism best delineated here is a result of virus-induced altered Aspergillus iron metabolism.

Journal article

Rashid K, Tariq M, Briddon RW, Kotta-Loizou I, Hussain Ket al., 2021, Identification and molecular characterization of rose leaf curl virus in ornamental pomegranate (Punica granatum L.), Australasian Plant Pathology, Pages: 1-4, ISSN: 0815-3191

Symptoms of leaf curling and yellowing, typical of begomoviruses, were observed on ornamental pomegranate plants in a park in Faisalabad, Pakistan. Leaves from symptomatic plants were collected and DNA extracted. PCR amplification with universal primers for the amplification of begomoviruses amplified an approx. 2.8 kb fragment which was cloned and sequenced. Similar amplifications with primers for begomovirus DNA B component and betasatellites were uniformly negative and no amplifications were obtained with DNA extracted from a non-symptomatic pomegranate plant. Sequence comparisons showed the cloned fragment to be an isolate of rose leaf curl virus (RoLCuV). This is the first time RoLCuV has been identified in a bushy shrub pomegranate. Sequence analysis shows the RoLCuV isolate from pomegranate to have a recombination history distinct from other RoLCV isolates.

Journal article

Filippou C, Diss R, Daudu J, Coutts R, Kotta-Loizou Iet al., 2021, The polymycovirus-mediated growth enhancement of the entomopathogenic fungus Beauveria bassiana is dependent on carbon and nitrogen metabolism, Frontiers in Microbiology, Vol: 12, ISSN: 1664-302X

Polymycoviridae is a growing family of mycoviruses whose members typically have non-conventional capsids and multi-segmented, double-stranded (ds) RNA genomes. Beauveria bassiana polymycovirus (BbPmV) 1 is known to enhance the growth and virulence of its fungal host, the entomopathogenic ascomycete and popular biological control agent B. bassiana. Here we report the complete sequence of BbPmV-3, which has six genomic dsRNA segments. Phylogenetic analysis of RNA-dependent RNA polymerase (RdRp) protein sequences revealed that BbPmV-3 is closely related to the partially sequenced BbPmV-2 but not BbPmV-1. Nevertheless, both BbPmV-3 and BbPmV-1 have similar effects on their respective host isolates ATHUM 4946 and EABb 92/11-Dm, affecting pigmentation, sporulation, and radial growth. Production of conidia and radial growth are significantly enhanced in virus-infected isolates as compared to virus-free isogenic lines on Czapek-Dox complete and minimal media that contain sucrose and sodium nitrate. However, this polymycovirus-mediated effect on growth is dependent on the carbon and nitrogen sources available to the host fungus. Both BbPmV-3 and BbPmV-1 increase growth of ATHUM 4946 and EABb 92/11-Dm when sucrose is replaced by lactose, trehalose, glucose, or glycerol, while the effect is reversed on maltose and fructose. Similarly, both BbPmV-3 and BbPmV-1 decrease growth of ATHUM 4946 and EABb 92/11-Dm when sodium nitrate is replaced by sodium nitrite, potassium nitrate, or ammonium nitrate. In conclusion, the effects of polymycoviruses on B. bassiana are at least partially mediated via its metabolic pathways.

Journal article

Vassilaki N, Frakolaki E, Kalliampakou KI, Sakellariou P, Kotta-Loizou I, Bartenschlager R, Mavromara Pet al., 2020, A Novel Cis-Acting RNA Structural Element Embedded in the Core Coding Region of the Hepatitis C Virus Genome Directs Internal Translation Initiation of the Overlapping Core+1 ORF, INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, Vol: 21

Journal article

Filippou C, Coutts RHA, Stevens DA, Sabino R, Kotta-Loizou Iet al., 2020, Completion of the sequence of the Aspergillus fumigatus partitivirus 1 genome, ARCHIVES OF VIROLOGY, Vol: 165, Pages: 1891-1894, ISSN: 0304-8608

Journal article

Engl C, Jovanovic G, Brackston RD, Kotta-Loizou I, Buck Met al., 2020, The route to transcription initiation determines the mode of transcriptional bursting in E. coli, Nature Communications, Vol: 11, ISSN: 2041-1723

Transcription is fundamentally noisy, leading to significant heterogeneity across bacterial populations. Noise is often attributed to burstiness, but the underlying mechanisms and their dependence on the mode of promotor regulation remain unclear. Here, we measure E. coli single cell mRNA levels for two stress responses that depend on bacterial sigma factors with different mode of transcription initiation (σ70 and σ54). By fitting a stochastic model to the observed mRNA distributions, we show that the transition from low to high expression of the σ70-controlled stress response is regulated via the burst size, while that of the σ54-controlled stress response is regulated via the burst frequency. Therefore, transcription initiation involving σ54 differs from other bacterial systems, and yields bursting kinetics characteristic of eukaryotic systems.

Journal article

Ye F, Kotta-Loizou I, Jovanovic M, Liu X, Dryden DT, Buck M, Zhang Xet al., 2020, Structural basis of transcription inhibition by the DNA mimic protein Ocr of bacteriophage T7., eLife, Vol: 9, ISSN: 2050-084X

Bacteriophage T7 infects Escherichia coli and evades the host restriction/modification system. The Ocr protein of T7 was shown to exist as a dimer mimicking DNA and to bind to host restriction enzymes, thus preventing the degradation of the viral genome by the host. Here we report that Ocr can also inhibit host transcription by directly binding to bacterial RNA polymerase (RNAP) and competing with the recruitment of RNAP by sigma factors. Using cryo electron microscopy, we determined the structures of Ocr bound to RNAP. The structures show that an Ocr dimer binds to RNAP in the cleft, where key regions of sigma bind and where DNA resides during transcription synthesis, thus providing a structural basis for the transcription inhibition. Our results reveal the versatility of Ocr in interfering with host systems and suggest possible strategies that could be exploited in adopting DNA mimicry as a basis for forming novel antibiotics.

Journal article

Kotta-Loizou I, Caston JR, Coutts RHA, Hillman B, Jiang D, Kim D-H, Moriyama H, Suzuki Net al., 2020, ICTV virus taxonomy profile: chrysoviridae, Journal of General Virology, Vol: 101, Pages: 143-144, ISSN: 0022-1317

Members of the family Chrysoviridae are isometric, non-enveloped viruses with segmented, linear, dsRNA genomes. There are 3–7 genomic segments, each of which is individually encapsidated. Chrysoviruses infect fungi, plants and possibly insects, and may cause hypovirulence in their fungal hosts. Chrysoviruses have no known vectors and lack an extracellular phase to their replication cycle; they are transmitted via intracellular routes within an individual during hyphal growth, in asexual or sexual spores, or between individuals via hyphal anastomosis. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the family Chrysoviridae, which is available at ictv.global/report/chrysoviridae.

Journal article

Shah UA, Kotta-Loizou I, Fitt BDL, Coutts RHAet al., 2020, Mycovirus-Induced Hypervirulence of Leptosphaeria biglobosa Enhances Systemic Acquired Resistance to Leptosphaeria maculans in Brassica napus, MOLECULAR PLANT-MICROBE INTERACTIONS, Vol: 33, Pages: 98-107, ISSN: 0894-0282

Journal article

Abdoulaye AH, Foda MF, Kotta-Loizou I, 2019, Viruses Infecting the Plant Pathogenic Fungus Rhizoctonia solani, VIRUSES-BASEL, Vol: 11

Journal article

Umer M, Liu J, You H, Xu C, Dong K, Luo N, Kong L, Li X, Hong N, Wang G, Fan X, Kotta-Loizou I, Xu Wet al., 2019, Genomic, Morphological and Biological Traits of the Viruses Infecting Major Fruit Trees, VIRUSES-BASEL, Vol: 11

Journal article

Kotta-Loizou I, Hadrien P, Saunders K, Coutts R, Lomonossoff Get al., 2019, Investigating the biological relevance of in vitro identified putative packaging signals at the 5’ terminus of the satellite tobacco necrosis virus-1 genomic RNA, Journal of Virology, Vol: 93, Pages: 1-18, ISSN: 1098-5514

Satellite tobacco necrosis virus-1 (STNV-1) is a model system for in vitro RNA encapsidation studies (Patel et al., PNAS 2015, 2017), leading to the identification of degenerate packaging signals (PSs) proposed to be involved in the recognition of its genome by the capsid protein (CP). The aim of the present work was to investigate whether these putative PSs can confer selective packaging of STNV-1 RNA in vivo and assess the prospects of using decoy RNAs in antiviral therapy. We have developed an in planta packaging assay based on the transient expression of STNV-1 CP and assessed the ability of the resulting VLPs to encapsidate mutant STNV-1 RNAs expected to have different encapsidation potential based on in vitro studies. The results revealed that >90% of the encapsidated RNAs are host-derived, although there is some selectivity of packaging for STNV-1 RNA and certain host RNAs. Comparison of the packaging efficiency of mutant STNV-1 RNAs showed that they are encapsidated mainly according to their abundance within the cells, rather than the presence or absence of the putative PSs previously identified from in vitro studies. By contrast, subsequent infection experiments demonstrated that host RNAs represent only <1% of virion content. Although selective encapsidation of certain host RNAs was noted, no direct correlation could be made between this preference and the presence of potential PSs in the host RNA sequences. Overall the data illustrate the differences in RNA packaging efficiency identified through in vitro studies are insufficient to explain the specific packaging of STNV-1 RNA.

Journal article

Kotta-Loizou I, 2019, Mycoviruses: Past, Present, and Future, VIRUSES-BASEL, Vol: 11, ISSN: 1999-4915

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Shah UA, Kotta-Loizou I, Fitt BDL, Coutts RHAet al., 2019, Identification, Molecular Characterization, and Biology of a Novel Quadrivirus Infecting the Phytopathogenic Fungus Leptosphaeria biglobosa, VIRUSES-BASEL, Vol: 11

Journal article

Filippou C, Garrido-Jurado I, Meyling NV, Quesada-Moraga E, Coutts RHA, Kotta-Loizou Iet al., 2018, Mycoviral Population Dynamics in Spanish Isolates of the Entomopathogenic Fungus Beauveria bassiana, VIRUSES-BASEL, Vol: 10

Journal article

Giaginis C, Sampani A, Kotta-Loizou I, Giannopoulou I, Danas E, Politi E, Tsourouflis G, Kouraklis G, Patsouris E, Keramopoulos A, Nakopoulou L, Theocharis Set al., 2018, Elevated Hu-antigen Receptor (HuR) expression is associated with tumor aggressiveness and poor prognosis but not with COX-2 expression in invasive breast carcinoma patients, Pathology and Oncology Research, Vol: 24, Pages: 631-640, ISSN: 1219-4956

Hu-antigen R (HuR), a RNA-binding protein, is considered to play a crucial role in tumor development and progression by stabilizing or regulating a group of cellular mRNAs of cancer-related genes, such as cyclooxygenase-2 (COX-2). The present study aimed to evaluate the clinical significance of HuR and COX-2 expression in invasive breast carcinoma. HuR and COX-2 protein expression was assessed immunohistochemically on paraffin-embedded breast cancer tissue sections obtained from 121 patients and was statistically analyzed with clinicopathological parameters, estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2), as well as with tumor cells' proliferative capacity and overall and disease-free patients' survival. High HuR expression was positively associated with larger tumor size and advanced disease stage (p = 0.0234 and p = 0.0361, respectively), being more frequently observed in ER negative cases (p = 0.0208). High COX-2 expression was negatively associated with histological (p < 0.0001) and nuclear (p = 0.0033) grade and tumor cells' proliferative rate (p = 0.0015), being more frequently observed in luminal-A compared to other molecular subtypes (p = 0.0221). High HuR expression was associated with poor overall and disease-free patients' survival at both univariate (log-rank test, p = 0.0092 and p = 0.0004, respectively) and multivariate (Cox-regression analysis, p = 0.0223 and p = 0.0004, respectively) level. On the other hand, high COX-2 expression was associated with favorable overall and disease-free patients' survival merely at univariate level (log-rank test, p = 0.0389 and p = 0.0154, respectively). HuR expression was not associated with COX-2 expression (Spearman R = 0.1489, p = 0.1032). The present data support evidence that HuR is associated with tumor ag

Journal article

Glyde R, Ye F, Jovanovic M, Kotta-Loizou I, Buck M, Zhang Xet al., 2018, Structures of bacterial RNA polymerase complexes reveal mechanisms of DNA loading and transcription initiation, Molecular Cell, Vol: 70, Pages: 1111-1120.e3, ISSN: 1097-2765

Gene transcription is carried out by multi-subunit RNA polymerases (RNAP).Transcription initiation is a dynamic multi-step process that involves the opening of the double stranded DNA to form a transcription bubble and delivery of the template strand deep into the RNAP for RNA synthesis. Applying cryo electron microscopy to a unique transcription system using 54 (N), the major bacterial variant sigma factor, we capture a new intermediate state at 4.1 Å where promoter DNA is caught at the entrance of the RNAP cleft. Combining with new structures of the open promotercomplex and an initial de novo transcribing complex at 3.4 and 3.7 Å respectively, our studies reveal the dynamics of DNA loading and mechanism of transcription bubble stabilisation that involves coordinated, large scale conformational changes of the universally conserved features within RNAP and DNA. In addition, our studies reveal a novel mechanism of strand separation by 54.

Journal article

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