Experimental rnomics
Loading...
Date
2008
Authors
Zakaria, Robaiza
Journal Title
Journal ISSN
Volume Title
Publisher
Abstract
Non-protein-coding RNA (npcRNA) is a large class of riboregulators that act in
complex with proteins (as RNPs) in diverse regulatory pathways. This thesis focused on
the experimental identification of small npcRNAs from Salmonella enterica serovar
Typhi (S. Typhi), the aetiological agent of typhoid fever. By an Experimental RNomics
approach, 82 species of uncharacterized novel npcRNA candidates were identified from
library generated from different growth phases of a clinically isolated S. Typhi. From
this, 28 were transcribed from the IGRs, 29 were transcribed in the antisense orientation
of the ORFs and 18 were identified to overlap the ORFs. Another 7 candidates were
transcribed from repetitive regions and several non-repetitive locations. Eleven known
npcRNAs were also detected. Interestingly, 55 candidates exhibit homology to
Escherichia coli and were not previously annotated for both organisms. By Northern Blot
analysis, the expression of 38 novel npcRNA candidates was confirmed. A total of 28
novel npcRNA candidates were growth phase regulated where 14 candidates were growth
phase regulated in both S. Typhi USM05 and E. coli K12, 11 candidates were speciesspecific
growth phase regulated only in S. Typhi USM05 and three candidates were
species-specific growth phase regulated only in E. coli K12. A total of 8 npcRNA
candidates were ubiquitously expressed with 6 candidates were ubiquitously expressed in
both S. Typhi USM05 and E. coli K12 and 2 candidates were species-specific
ubiquitously expressed only in S. Typhi USM05. There was no species-specific
ubiquitously expressed candidate observed in E. coli K12. Two out of 38 candidates were
shown to be growth phase regulated and ubiquitously expressed. The different feature of
expression patterns observed in this study can be associated with the different classes of
npcRNA that they might be grouped-in, namely the housekeeping and the regulatory
npcRNAs. A number of novel npcRNA candidates were shown to be located close to
important genes that were conserved in E. coli K12 and among Salmonella. Thus,
suggesting that they might be functionally important. Significantly, this study has set the
understanding on the importance of the specific growth conditions to the expression of
npcRNAs. The next phases of challenge are to further characterize and to elucidate the
functions of these new classes of small RNA molecules. Considering that such regulators
may be highly expressed upon induction, these molecules may be greatly enriched in
cDNA libraries prepared from the relevant growth or stress condition.
Description
PhD
Keywords
Biological Science , Rnomics , Ribonucleic acids , Pathogenic agent