ΠΜΣ Βιοπληροφορική
Library of the School of Science

2012-02-02

2012

Σαββάκης Ιωάννης

Παππά Κ.Μ. Επικ. Καθηγ.(Επιβλέπουσα), Χαμόδρακας Σ. Καθηγ., Μπάγκος Π. Επικ. Καθηγ.

Μελέτη της επιδιόρθωσης του DNA στο αιθανολοπαραγωγό βακτήριο Zymomonas mobilis

Greek

Zymomonas mobilis is an α-proteobacterium with a great potential for industrial
bioethanol
production. Its tolerance to stress is of particular interest, since it entails
adapting to and
performing in challenging bioprocessing environments. Genes induced by stress
include
DNA-repair genes and are often coordinately expressed. A major example is given
by the
SOS regulon of E. coli, which is governed by the RecA/LexA proteins and
comprises of
dozens of co-transcribed genes.
In this work, an in silico analysis was employed to identify genes orthologous
to that of
enterobacterial or α-proteobacterial SOS systems, in two different Z. mobilis
strain genomes
(ATCC31821/ZM4 and NCIMB 11163; GenBank acc. No. AE008692 and CP001722), via
use of latest gene-calling designations and BLAST similarity searches.
Moreover, indications
for coordinate regulation were sought, based on the conservation of the α-
proteobacterial
LexA-binding SOS-box [G(T/A)(T/A)CN7G(T/A)(T/A)C] that lies upstream from
regulon
members. For this, a C language program developed in our lab and FITOM
(http://compbio.umbc.-edu/9466/) were used to search for SOS-box conservation
upstream
from expected SOS genes and in whole genomes. Lastly, conserved motif search in
the Z.
mobilis RecA and LexA proteins was carried out by ClustalW alignments, relying
on previous
biochemical data offered by the E. coli counterparts.
The Z. mobilis RecA and LexA proteins seem functionally conserved, which
indicates their
possible implication in SOS regulation for this bacterium. Approximately 40
DNA-repair
gene candidates were found in each examined genome, at least 8 of which bearing
SOS boxes
with no (recA and lexA) or one consensus mismatch, and a considerable number
with two or
more mismatches. An interesting finding of whole-genome scans was that SOS-box
motifs
with zero to one base substitution precede approximately 70 genes irrelevant to
DNA repair
(genes for metabolism, protein synthesis, tolerance to organic agents or
transcriptional
regulation), which indicates that the SOS regulon of Z. mobilis may be broader
than thought.

Zymomonas mobilis, SOS response, DNA Repair, Transcriptional regulation, Bioethanol

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https://pergamos.lib.uoa.gr/uoa/dl/object/1318595