| Summary: | Thesis (PhD)--Stellenbosch University, 2015. === ENGLISH ABSTRACT: Mycoplasma nasistruthionis sp. nov. str. Ms03 (Ms03) is one of three Mycoplasma species
that were identified from ostriches. Mycoplasmas infections have been implicated in ostrich
chick mortalities, growth retardation and downgrading of ostrich carcasses. Currently there is
no vaccine available for the treatment of mycoplasmosis in ostriches. This study investigated
the development of DNA vaccines against Ms03 infections in ostriches. To this end, the
Ms03 genome was sequenced and annotated. The vaccine candidate gene, oppA, was
identified within the genome sequence and characterized before DNA vaccines containing
the oppA were developed and tested. The genome of Ms03 was sequenced and the resulting 172 contigs were annotated. This
dissertation presents the first Ms03 draft genome and annotation which contributed to the
understanding of Ms03 as a miniature genetically independent organism. In Ms03, genome
replication, cell division, RNA transcription, protein translation and glycolysis resemble that
of the closely related Mycoplasma synoviae 53. Purine and pyrimidine metabolism was
incomplete and de novo synthesis thereof was not possible. Amino acid synthesis in Ms03
was mostly absent and only the genes that convert aspartate to asparagine and glycine to
serine were found. More importers than exporters were annotated owing to the lack of
synthesis pathways in Ms03, which is typical for mycoplasmas that have parasitic life styles.
Two oligopeptide permease (opp) operons were annotated within the Ms03 genome. The potential of the oppA as a vaccine candidate gene was evaluated by investigating the
need for a substrate-binding domain (OppA) as part of the OppBCDF transporter within
Mycoplasma species. An oppA homologue could be identified for each oppBCDF operon in
all species and therefore must play an essential role in oligopeptide transport. All
mycoplasmas (except for hemoplasma) had one, two or three opp operons that could be
divided into three types (Type A, B and C). Each type had unique InterPro and MEME
domains and motifs which together with the phylogenetic analysis suggest unique roles in
their survival under different conditions. Ms03 had a Type A and a Type B opp operon, the
Type A oppA was used as vaccine candidate gene. The Type A oppA was cloned and site-directed mutagenesis was used for codon correction
before the mutated gene was sub-cloned into three DNA vaccine vectors. The three DNA
vaccines (pCI-neo_oppA, VR1012_oppA and VR1020_oppA) were used to vaccinate
ostriches and the OppA-antibody response was analysed by ELISA. The VR1020_oppA and
pCI-neo_oppA constructs elicited a primary immune response in ostriches, indicating that
the OppA protein was expressed in vivo and was immunogenic. This can therefore be
viewed as the first step in the development of a DNA vaccine for the control of mycoplasma
infections in ostriches. === AFRIKAANSE OPSOMMING: Mycoplasma nasistruthionis sp. nov. str. Ms03 (Ms03) is een van drie mikoplasma spesies
wat volstruise infekteer. Mikoplasma-infeksies in volstruise veroorsaak kuiken vrektes,
vertraagde groei en afgradering van volstruis karkasse. Daar is tans geen geregistreerde
mikoplasma entstof beskikbaar vir gebruik in volstruise nie. Hierdie studie het die
ontwikkeling van DNS-entstowwe teen Ms03-infeksies in volstruise ondersoek. Vir hierdie
doel was die Ms03-genoomvolgorde bepaal en geannoteer. Die entstofkandidaat-geen,
oppA, was geïdentifiseer in die genoomvolgorde en gekarakteriseer voordat DNS-entstowwe
(wat die oppA-geen bevat) ontwikkel en getoets is. Die Ms03-genoomvolgorde was bepaal en die gegenereerde 172 aaneenlopende volgordes
was geannoteer. Hierdie proefskrif bied die eerste voorlopige volgorde en annotering van die
Ms03-genoom wat bygedra het tot die kennis van Ms03 as 'n miniatuur geneties
onafhanklike organisme. Genoom-replikasie, seldeling, RNS-transkripsie, proteïen-translasie
en glikolise in Ms03 stem ooreen met dié prosesse in die naverwante Mycoplasma synoviae
53. Die purien en pirimidien metabolisme was onvolledig en de novo sintese daarvan was
nie moontlik in Ms03 nie. Aminosuursintese in Ms03 was meestal afwesig en net die gene
wat aspartaat omskep na asparagien en glisien na serien was gevind in die annoteerde
genoom. Meer invoerders as uitvoerders was geannoteer, wat dui op die gebrek aan
sintesepadweë in Ms03. Dit is tipies van mikoplasmas wat ‘n parasitiese lewensstyle het.
Twee oligopeptied-permeases (opp) operons was gevind in die Ms03-genoom. Die potensiaal van die oppA-geen as 'n entstofkandidaat-geen was geëvalueer deur die
behoefte van 'n substraatbindingsdomein (OppA) as deel van die OppBCDF-vervoerder
binne mikoplasma spesies te ondersoek. 'n Homoloog van die oppA-geen kon geïdentifiseer
word vir elke oppBCDF-operon in al die spesies en behoort daarom 'n noodsaaklike rol te
speel in die vervoer van oligopeptiede. Alle mikoplasmas (behalwe vir hemoplasmas) het
een, twee of drie opp-operons, wat verdeel kan word in drie tipes (Tipe A, B en C). Elke tipe
het unieke InterPro en MEME domeine en motiewe wat saam met die filogenetiese ontleding
daarop dui dat hulle unieke rolle in oorlewing onder verskillende omstandighede speel. Ms03
het 'n Tipe A en Tipe B opp-operon, die Tipe A oppA is gebruik as entstofkandidaat-geen. Die Tipe A oppA-geen was gekloneer en teikengerigte-mutagenese was gebruik vir
kodonregstellings voordat die gemuteerde geen in drie DNS-entstof vektore gesubkloneer
was. Die drie DNS-entstowwe (pCI-neo_oppA, VR1012_oppA en VR1020_oppA) was
gebruik om volstruise in te ent en die OppA-teenliggaamsreaksie was geanaliseer deur
ELISA. Inenting met die VR1020_oppA en pCI-neo_oppA entstowwe het tot 'n primêre
immuniteitsreaksie in volstruise gelei. Dit dui daarop dat die OppA proteïen in vivo uitgedruk
en immunogenies was. Dit kan beskou word as die eerste stap in die ontwikkeling van 'n
DNS-entstof vir die beheer van mikoplasma-infeksies in volstruise.
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