Pseudogenes are defined as coding regions disrupted by frameshifts or internal stop codons, identifiable by their similarity to characterized genes in other sequences, but unlikely to be functional owing to the disruption. Pseudogenes for Las Psy62 (CP001677) were identified and assigned product numbers by Duan, et al. MPMI 22:1011-1020 supplemental Table S2 (abstract) but not all are included in the annotation file at NCBI.
Locations of the unannotated pseudogenes have been identified by BLAST analysis of unannotated gaps in the deposited sequence. Coordinates and product descriptions are shown in the table below
Two categories of pseudogenes are of particular interest:
- genes generally considered to be essential for viability
(e.g. disruption of DNA polymerase III subunits and lipoprotein transport system)
- genes for which disruption may highlight important aspects of Las Psy62 evolution and niche-adaptation
(e.g. disruption of amino acid biosynthetic genes and miaA gene)
|
pseudogene product number |
pseudogene product name |
included in NCBI annotation |
|
|
generally essential for viability
|
role of product in cell |
CLIBASIA_00170 |
D-3-phosphoglycerate dehydrogenase protein |
no |
complement (34536..36088)
|
no |
no |
catalyzes first committed step in biosynthesis of L-serine, disruption is consistent with loss of amino acid biosynthetic capabilities |
CLIBASIA_00360 |
ribonucleotide reductase, subunit beta |
no |
|
CLIBASIA_03700 (intact) |
yes |
catalyzes the formation of deoxyribonucleotides from ribonucleotides, paralogs within a single genome unprecedented |
CLIBASIA_01850 |
acetylglutamate kinase protein |
no |
406271..407154 |
no |
no |
required for arginine biosyntheis, disruption is consistent with loss of amino acid biosynthetic capabilities |
CLIBASIA_03575 |
double-strand break repair helicase AddA |
no |
430017..433575 |
no |
no |
Performs a critical step in DNA repair as part of the SOS response (PMID: 15547262) |
CLIBASIA_03270 |
DNA polymerase III subunits gamma/tau |
no |
499568..501134 |
no |
yes |
required for formation of the clamp loader complex (PMID: 11525729) |
CLIBASIA_03250 |
peptidoglycan lipid II flippase MurJ/MviN |
no |
502461..504037 |
CLIBASIA_03420 (intact) |
yes in E. coli
no in B. subtilis |
required for peptidoglycan synthesis
in E. coli (PMID: 18832143) |
CLIBASIA_03635 |
DNA polymerase III alpha subunit |
no |
797696..801329 |
no |
yes |
catalysis of DNA polymerase in replication (PMID: 17531796) |
CLIBASIA_03830 |
lipoprotein releasing system, transmembrane protein, LolC/E family |
no |
841098..842352 |
no |
yes in E. coli
(PMID: 11844772) |
required for ABC-dependent transport of outer membrane-specific lipoproteins in E. coli (PMID: 19307584) |
CLIBASIA_03985 |
RadC |
no |
complement (874850..875562) |
no |
no |
highly conserved protein of unknown function (PMID: 18556794) |
CLIBASIA_04300 |
tRNA delta(2)-isopentenylpyrophosphate transferase protein (miaA) |
no |
958373..959285 |
no |
no |
catalyzes the addition of an isopentenyl moiety onto the N-6 atom of adenosine in position 37 of UNN species tRNAs. Mutation of E. coli miaA results in mutator phenotype with increased incidence of GC->AT transversions (PMID: 1999389) |
CLIBASIA_05220 |
putative phage head protein |
no |
complement (1138874..1139868) |
- |
- |
phage assembly |
CLIBASIA_05260 |
probable DNA packaging protein GP2 |
no |
complement (1142729..1144168) |
- |
- |
phage assembly |
