Characterisation and Classification of Protein Sequences by Using Enhanced Amino Acid Indices and Signal Processing-Based Methods

Due to copyright reasons, the authors published papers have been removed from this copy of the thesis.Protein sequencing has produced overwhelming amount of protein sequences, especially in the last decade. Nevertheless, the majority of the proteins' functional and structural classes are still unknown, and experimental methods currently used to determine these properties are very expensive, laborious and time consuming. Therefore, automated computational methods are urgently required to accurately and reliably predict functional and structural classes of the proteins. Several bioinformatics methods have been developed to determine such properties of the proteins directly from their sequence information. Such methods that involve signal processing methods have recently become popular in the bioinformatics area and been investigated for the analysis of DNA and protein sequences and shown to be useful and generally help better characterise the sequences. However, there are various technical issues that need to be addressed in order to overcome problems associated with the signal processing methods for the analysis of the proteins sequences. Amino acid indices that are used to transform the protein sequences into signals have various applications and can represent diverse features of the protein sequences and amino acids. As the majority of indices have similar features, this project proposes a new set of computationally derived indices that better represent the original group of indices. A study is also carried out that resulted in finding a unique and universal set of best discriminating amino acid indices for the characterisation of allergenic proteins. This analysis extracts features directly from the protein sequences by using Discrete Fourier Transform (DFT) to build a classification model based on Support Vector Machines (SVM) for the allergenic proteins. The proposed predictive model yields a higher and more reliable accuracy than those of the existing methods. A new method is proposed for performing a multiple sequence alignment. For this method, DFT-based method is used to construct a new distance matrix in combination with multiple amino acid indices that were used to encode protein sequences into numerical sequences. Additionally, a new type of substitution matrix is proposed where the physicochemical similarities between any given amino acids is calculated. These similarities were calculated based on the 25 amino acids indices selected, where each one represents a unique biological protein feature. The proposed multiple sequence alignment method yields a better and more reliable alignment than the existing methods. In order to evaluate complex information that is generated as a result of DFT, Complex Informational Spectrum Analysis (CISA) is developed and presented. As the results show, when protein classes present similarities or differences according to the Common Frequency Peak (CFP) in specific amino acid indices, then it is probable that these classes are related to the protein feature that the specific amino acid represents. By using only the absolute spectrum in the analysis of protein sequences using the informational spectrum analysis is proven to be insufficient, as biologically related features can appear individually either in the real or the imaginary spectrum. This is successfully demonstrated over the analysis of influenza neuraminidase protein sequences. Upon identification of a new protein, it is important to single out amino acid responsible for the structural and functional classification of the protein, as well as the amino acids contributing to the protein's specific biological characterisation. In this work, a novel approach is presented to identify and quantify the relationship between individual amino acids and the protein. This is successfully demonstrated over the analysis of influenza neuraminidase protein sequences. Characterisation and identification problem of the Influenza A virus protein sequences is tackled through a Subgroup Discovery (SD) algorithm, which can provide ancillary knowledge to the experts. The main objective of the case study was to derive interpretable knowledge for the influenza A virus problem and to consequently better describe the relationships between subtypes of this virus. Finally, by using DFT-based sequence-driven features a Support Vector Machine (SVM)-based classification model was built and tested, that yields higher predictive accuracy than that of SD. The methods developed and presented in this study yield promising results and can be easily applied to proteomic fields

Characterisation of two desiccation-linked dehydrins from Xerophyta humilis

In response to abiotic stresses, organisms throughout the plant kingdom, as well as microorganisms and micro-animals such as nematodes or tardigrades, have been observed to express Late Embryogenesis Abundant (LEA) proteins as protective mechanisms. However, despite two decades of research, little is understood about their physiological functions and this has led to extensive nomenclature, with a large amount of redundancy. The primary reason for this lack of insight into LEA protein functions is their highly hydrophilic and intrinsically disordered nature. Intrinsically disordered proteins (IDPs) cannot be studied using conventional methods of structural analyses such as X-ray crystallography and, therefore, alternative techniques are required. A combination of transgenic and in vitro studies have also shown that LEA proteins are most likely to behave as molecular chaperones by binding water and ions, preventing macromolecular aggregation and protecting enzymatic activity during dehydration. This study characterized two dehydrins that were expressed during dehydration in the desiccation tolerant plant, Xerophyta humilis. From a transcriptome analyses on X. humilis, cDNA for the two dehydrins were obtained. These sequences were first analysed using various in silico tools in order to identify putative dehydrin-specific characteristics. Subsequently, these two dehydrins were cloned and expressed for production of recombinant dehydrin protein. These proteins were then analysed in terms of structural and functional characteristics. Structurally, through the use of circular dichroism in an in vitro system, both dehydrins demonstrated the shift towards being increasingly alpha-helical when placed in environments of decreasing water content. The role of these two dehydrins in stabilizing enzymes during dehydration was subsequently investigated using citrate synthase (CS) and lactate dehydrogenase (LDH). The preservation of enzyme activity was observed in both CS and LDH. This preservation of enzyme activity was further maintained by the presence of trehalose. Anti-aggregation roles were also investigated, however, neither dehydrin demonstrated significant ability to minimize the aggregation of LDH. This study hopes to establish a pipeline for characterizing LEA proteins using structural and functional assays in order to provide alternative means of LEA protein classification

Macrophage activating factor (MAF) in rainbow trout (Oncorhynchus mykiss) : biological activity and molecular source

This study investigated the biological activity of a macrophage activating factor (MAF) produced by activated lymphocytes from the rainbow trout (Oncorhynchus mykiss) and attempts to discover its molecular source. Peripheral blood lymphocytes were shown to release factors with MAF activity following incubation with a variety of stimulants and were subsequently shown to activate macrophages using at least two different methods, the nitroblue tetrazolium (NBT) colourimetric assay and the luminol-dependent chemiluminescent assay. The latter technique detected an immediate response which decayed over a 40 minute period on the addition of cell-free supernatants from activated lymphocytes to macrophages. A number of molecular approaches, including degenerate PCR primer amplification, DNA cross-hybridisation and cDNA library screening were used in this study to try to isolate any cytokine genes from Oncorhynchus mykiss. As a control β-actin cDNA was successfully amplified from Oncorhynchus mykiss using primers based on the salmon sequence. The Oncorhynchus mykiss orthologue of IFN-y was initially targeted. However, although a PCR product of the appropriate size was amplified using degenerate primers based on mammalian and avian IFN-y sequences, the sequence was not related to IFN-y or any other known Oncorhynchus mykiss sequence. A similar strategy was used to try and amplify the Oncorhynchus mykiss orthologue of mammalian IL-15. Again despite amplification of a DNA fragment of approximately the correct size there appeared to be no relationship between it and the known IL-15 sequences. As an alternative strategy a cDNA library from stimulated peripheral blood lymphocytes (PBLs) was constructed and screened using cDNA probes derived from stimulated and non-stimulated PBLs in order to detect mRNAs which might have been upregulated as a result of in vitro stimulation. A number of positive clones were obtained from the differential screening of the library including cDNAs showing similarity to other unidentified fish sequences as well as to a number of proteins predicted to be involved in regulation of cell proliferation, neocorticogenesis and embryo development. Additionally. the library was also screened using ovine cytokine cDNA probes. although no positively hybridising clones were obtained. The ovine IFN-y gene was also used to probe genomic DNA from Oncorhynchus mykiss. but unlike previous studies with human IFN-y gene no hybridisation between the ovine IFN-y gene and Oncorhynchus mykiss DNA was observed. This investigation highlights the potential difficulties of using various molecular strategies such as DNA cross-hybridisation or PCR techniques for the cloning of fish cytokine sequences. Consequently, future strategies for cloning fish cytokine genes may require targeting the biological activity through expression libraries

Silencing parasitism effectors of the root lesion nematode, Pratylenchus thornei

The root lesion nematode (RLN), Pratylenchus thornei, is a biotrophic migratory pest of plant roots and its infestation causes losses in many economically important crops. RNA interference (RNAi) is a naturally occurring eukaryotic phenomenon and can be used to silence parasitism effector genes of P. thornei using host-mediated RNAi. This may be developed as an environmentally friendly and a cost-effective control strategy. The overall aims of this research were to investigate the effects of in vitro and in planta RNAi silencing of putative P. thornei parasitism effector genes, and their nematicidal effects in two host plants. Five putative target parasitism genes vital for nematode entry into roots (Pt-Eng-1, Pt-PL), feeding (Pt-CLP) and suppressing host defence responses (Pt-UEP, Pt-GST) were identified, validated in silico using comparative bioinformatics, cloned into suitable in vitro transcription and binary vectors, and advanced to RNAi studies. Partial sequences for four of these target effector genes (Pt-Eng-1, Pt-PL, Pt-CLP, Pt-GST) were identified using Rapid Amplification of cDNA (RACE) PCRs and annotated in silico. Protein families, conserved domains, taxonomic and phylogenetic relationships for all four effectors were studied. This sequence information will help inform future investigations involving gene expression and proteomics of the selected putative effectors. In vitro RNAi was used for functional characterisation of the five effector sequences. Effects on nematode phenotype, behaviour, gene expression, and longer-term effects on reproduction were assessed after soaking nematodes in dsRNA through infection of healthy wild type soybean and alfalfa roots. Soaking of mixed stage P. thornei in 1mg/mL dsRNA of target genes for 16 h did not cause phenotypic changes except for Pt-PL, which exhibited straight or slightly curved phenotypes after soaking compared to the normal sigmoid body movement, also evident for green fluorescent protein (gfp) and no dsRNA treated controls. Semi-quantitative PCRs and densitometry analysis revealed a significant reduction of transcript accumulation for all five putative parasitism effector genes. Longer-term effects assessed at 21 dpi reduced nematode reproduction by 40 to 70% for all target genes compared to respective control treatments suggesting that the effectors studied were required for nematode infectivity, survival or reproduction. In planta RNAi involved Agrobacterium-mediated plant transformations to develop axenic transgenic hairy root events of soybean (Glycine max var. Williams 82) and alfalfa (Medicago sativa), and non-axenic hairy roots (composite plants) of soybean. Both hosts were amenable to Agrobacterium-mediated transformation, but hairy root induction was faster in alfalfa than soybean. However, more events were generated for soybean than alfalfa. Transgenic hairy roots confirmed by molecular analyses were challenged with P. thornei and their presence confirmed after 14 dpi. After 21 dpi, nematode numbers and transcript abundance was assessed using semi-quantitative PCRs and densitometry analysis. Host-mediated silencing of the five putative parasitism effector genes using transgenic soybean and alfalfa hairy roots showed a significant reduction in target transcript accumulation and approximately 38 to 75% reduction in P. thornei numbers compared to untransformed wild-type controls. For some events, there was a positive correlation between reduced transcripts and nematode numbers. Based on percent reduction in transcript accumulation of the target genes relative to 18S rRNA as assessed by densitometry, the extent of gene knockdown measured (from most to least) was: Pt-Eng-1, Pt-PL, Pt-CLP, Pt-UEP, and Pt-GST. Similarly, Pt-Eng-1, Pt-PL and Pt-CLP were ranked in the same order, from the lowest to highest reproduction on soybean and alfalfa, indicating a positive correlation between the level of knockdown and reduced reproduction. In soybean, these genes were followed by Pt-GST and Pt-UEP for the percentage of reproduction recorded, whereas, in alfalfa, reduction in reproduction for these two target genes did not differ significantly. Composite soybean with wild-type shoots and transgenic hairy roots expressing Pt-Eng-1 and Pt-PL genes were developed and provided an opportunity to test the effectiveness of silencing target genes in planta and on nematode numbers in conditions that mimicked natural host infections. For both Pt-Eng-1 and Pt-PL genes, there was a significant reduction in percentage of transcript accumulation relative to 18S rRNA, which correlated with a reduction in nematode numbers by 53.4% and 48.5% for Pt-Eng-1 and Pt-PL, respectively. The amenability of P. thornei to host-mediated RNAi using effector gene sequences, and the overall results of this study, point towards the potential use of this technology to control P. thornei and related RLN species effectively in different host crops

Investigation of particulate HIV-1 Env vaccine candidates using Zera® and SpyTag/SpyCatcher technologies

The HIV-1 envelope glycoprotein (Env) is the primary focus of prophylactic HIV vaccine development. However, the unusually low density of Env spikes on the virion (≈14 spikes/virion) is unfavourable for eliciting high titre, long-lasting antibody responses. It is possible that increasing the Env spike density of particulate vaccine candidates generated by protein body formation or via the display of Env on nanoparticles could improve the induction of long-lasting neutralising antibodies (NAbs). For this thesis, two different nanoparticle approaches were therefore investigated. The HIV-1 Env sequence used for both approaches was derived from the superinfecting subtype C CAP256 virus. This was truncated to remove the transmembrane domain, and engineered to contain a flexible linker (FL) in place of the furin cleavage site and an I559P mutation to generate soluble, stable and cleavageindependent gp140 proteins. The first approach investigated the impact of genetically fusing a 27 kDa proline-cysteine-rich domain of the ɣ-zein maize seed storage protein - Zera® - to either the N- or C-terminus of CAP256 gp140. Fusion of Zera® to a protein of interest can promote the self-assembly of large protein bodies (PBs) containing the protein of interest, thereby improving yields of the recombinant protein and enabling easy isolation using gradient ultracentrifugation. The purification of Zera-induced Env PBs from infiltrated Nicotiana benthamiana plants was not optimal. Consequently, the generation of Zera®-induced gp140 protein bodies was evaluated in a mammalian expression system. Stable HEK293 cell lines expressing Zera®-gp140 or gp140-Zera® were generated. A mixture of small PB-like structures was observed in cells expressing gp140-Zera®. However, no PB-like structures were seen in cells expressing Zera®-gp140. The immunogenicity of Zera®-gp140 and gp140-Zera® was evaluated by in rabbits. Binding and Tier 1A neutralising serum titres were higher for gp140-Zera® than for Zera®-gp140. Neither gp140-Zera® nor Zera®-gp140-specific sera neutralised a Tier 1B pseudovirus or the autologous Tier 2 CAP256SU pseudovirus, suggesting that Zera® might have compromised the structure of the Zera®-tagged gp140 proteins. The second approach investigated the two-component SpyCatcher/SpyTag technology. The stable HEK293 cell line expressing CAP256 gp140-SpyTag (gp140-ST) was generated, and trimers were purified to homogeneity using gel filtration. SpyCatcher (SC)-AP205 VLPs were produced in E. coli and purified by ultracentrifugation. The gp140-ST trimers and the SCAP205 VLPs were mixed in varying molar ratios to generate VLPs displaying the glycoprotein (AP205-gp140-ST particles). SDS-PAGE, dynamic light scattering and negative stain electron microscopy indicated that gp140-ST was successfully bound to the VLPs, although not all potential binding sites were occupied. The immunogenicity of the coupled VLPs was evaluated in a pilot study in rabbits. One group was injected four times with coupled VLPs. The second group was primed with DNA vaccines expressing Env and a mosaic Gag, followed by modified vaccinia Ankara expressing the same antigens and then boosted twice with coupled VLPs. Encouragingly, gp140-ST displayed on SC-AP205 VLPs was an effective boost to heterologously primed rabbits, leading to induction of autologous Tier 2 neutralising antibodies in 2/5 rabbits. These results demonstrate that careful selection of a geometrically-suitable nanoparticle scaffold to achieve a high-density display of HIV-1 envelope trimers is an important consideration and that this could improve the effect of nanoparticle-displayed gp140

Characterisation of immune responses to the E5 protein of the human papillomavirus type 16

A thesis submitted to the University of Luton for the degree of Doctor of PhilosophyHigh-risk mucosal human papillomaviruses (HPVs) are major aetiological agents for the development of cervical cancer. Thus, the current goal of cervical cancer treatment is to develop vaccines against HPV s. Such vaccines would either prevent cervical cancer by eliminating HPV infection or be useful for treating established lesions by the destruction of cells displaying HPV proteins. The aim of this thesis was to characterise immune responses to the E5 protein of HPV -16, one of several antigens with possible use in vaccination. To determine whether immune responses to HPV -16 E5 existed and whether they could be correlated with disease severity or with the presence of HPV -16 DNA, both cell mediated (Chapter Two) and humoral (Chapter Three) immunity was investigated in women with and without cervical disease. Cellular responses in a minority of women were inversely correlated with disease severity. However, E5 specific antibodies were negatively correlated with the absence of HPV -16 DNA. Thus, although some immune responses were evident, these were generally limited to a small number of subjects and were not associated with the detection of HPV-16 E5 mRNA or DNA sequence variants. Due to the immune responses in women, E5 was further investigated to determine if the absence of HPV -16 E5 specific immune responses was due to the poor antigenicity of HPV -16. Mice were immunised with synthetic peptides corresponding to full length HPV -16 E5 (Chapter Four). As with the human data, cellular responses and weak antibody responses were detected in mice. Some mice also exhibited cytotoxic T -lymphocyte responses and when E5/major histocompatibility class I (MHC-I) interactions were investigated, a number of peptides showed a high percentage of binding. The E5/MHC-I interactions were further investigated (Chapter Five). The surface expression of MHC-I on cells containing HPV-16 or -18 DNA was found to be lower than on HPV DNA negative cell lines even after stimulation with interferon-gamma. Stimulation with E5 synthetic peptides increased expression of cell surface MHC-I molecules on cell lines negative for HPV DNA. Furthermore, the presence of the E5 gene reduced the expression of the ovalbumin gene in normal human keratinocytes. In conclusion, the data contained within this thesis indicate that HPV-16 E5 CMI is inversely correlated with disease status. It is possible to induce cell mediated responses to HPV -16 E5 and low-titre antibody responses. The presence of HPV16 E5 DNA may impair normal cellular function

Characterisation of avian isolates of Staphylococcus aureus

The main part of the work was to develop PCR techniques for identification and typing of avian S. aureus. Different primer sets were applied in order to generate reproducible profiles of the PCR amplimers. Of the 86 avian S. aureus studied, 12, 7, 4 and 5 groups were recognised by the use of ribosomal, REP, coagulase gene and protein A gene primers respectively. PCR-ribotyping (method 1) produced a relatively simple pattern which was used for rapid identification of these isolates and for differentiation of these isolates from each other. These PCR fingerprinting methods were simple to perform and reproducible. The majority (80%) of the strains even from different geographical locations had similar “typical avian” profiles whereas 20% had atypical avian profiles. Results showed that many of the virulence factors characterised in this study in avian S. aureus were likely to be regulated by the agr and sar loci. Sequencing of the agrD region in selected strains suggested that 80% of avian (typical avian) isolates belonged to agr specificity group II and the other (20%) (atypical avian) stains belonged to agr specificity groups I or III. An investigation by multiplex PCR for eight toxin genes (encoding enterotoxins A-E, exfoliative toxins A-B and toxic shock syndrome toxin-1) revealed that only 5% of the avian isolates produced one or more of these toxin genes and all were atypical by other criteria. A multiplex PCR developed to detect haemolysin (a, g and d) genes showed that all the 86 avian S. aureus isolates had the a and d-haemolysin genes and a majority (86%) of the strains also had the g-haemolysin gene. Many of those that lacked the g-haemolysin gene were atypical by other criteria. Only 5% of the avian S. aureus strains possessed the b-haemolysin gene and, again, these isolates were atypical by other criteria