Table 3.
Genomes with unusual smpB content.
| smpB | Strain | tmID |
|---|---|---|
| BACTERIAL STRAINS WITH PSEUDOGENIZED, FRAMESHIFTED OR TRUNCATED smpB | ||
| Pseudogene | Hodgkinia cicadicola TETUND1* | 19190 |
| Truncation | Tremblaya princeps PCIT* | 12215 |
| Truncation | Tremblaya princeps PCVAL* | 12077 |
| Frameshift | Corynebacterium pseudotuberculosis 31 | 11952 |
| Frameshift | Mycobacterium intracellulare MOTT-2 | 19171 |
| Frameshift | Clostridium difficile CF5 | 10063 |
| Frameshift | Clostridium difficile M120 | 15031 |
| Frameshift† | Buchnera aphidicola BCc* | 15428 |
| Frameshift | Buchnera aphidicola str. TLW03* | 12194 |
| Frameshift | Pectobacterium carotovorum PCC21 | 16329 |
| Frameshift | Aggregatibacter actinomycetemcomitans ANH9381 | 19118 |
| Frameshift | Pseudomonas putida DOT-T1E | 10352 |
| Frameshift | Simiduia agarivorans SA1 | 19172 |
| Frameshift | Mycoplasma pneumoniae FH | 16792 |
| Frameshift | Thermotoga maritima MSB8 | 12964 |
| Frameshift | Petrotoga mobilis SJ95 | 13623 |
| smpBs IN BACTERIAL PLASMIDS | ||
| Flavobacterium sp. KI723T1 plasmid pOAD2 (2 copies) | 19173 | |
| smpBs IN EUKARYOTIC GENOME PROJECTS | ||
| Contaminant | Cucumis sativus | 19176 |
| Contaminant | Ceratitis capitata | 19177 |
| Endosymbiont | Trichoplax adhaerens | 19178 |
| Chromatophore | Paulinella chromatophora | 19174 |
| Oomycete mito.-targeted | Albugo laibachii Nc14gi | 19187 |
| Oomycete mito.-targeted | Phytophthora infestans T304 | 19188 |
| Oomycete mito.-targeted | Phytophthora sojae | 19189 |
| Algal plastid-targeted | Nannochloropsis gaditana CCMP526 | 19175 |
| Algal plastid-targeted | Guillardia theta CCMP2712 | 19179 |
| Algal plastid-targeted | Phaeodactylum tricornutum CCAP 1055/1 | 19180 |
| Algal plastid-targeted | Thalassiosira pseudonana CCMP1335 | 19181 |
| Algal plastid-targeted | Aureococcus anophagefferens | 19182 |
| Algal plastid-targeted | Callosobruchus chinensis | 19183 |
| Algal plastid-targeted | Cyanidioschyzon merolae | 19184 |
| Algal plastid-targeted | Ectocarpus siliculosus | 19185 |
| Algal plastid-targeted | Thalassiosira oceanica | 19186 |
Includes links to webpages for bacterial strains with defective smpBs, bacterial plasmids with smpBs, and smpBs in eukaryotic genome projects (some of which are organelle-targeted). The Hodgkinia genome pseudogene has accumulated two premature stop codons in smpB. The two “truncation” cases have lost material reaching into the β-barrel at each end. We also note that SmpB lacks the central loop in the hemoplasmas, Carsonella and Hodgkinia, and lacks the C-terminal α helix in Carsonella, but these SmpBs retain all β strand segments and may therefore retain weak function. tmID is the tmRNA Website (http://bioinformatics.sandia.gov/tmrna) identifier.
Highly reduced genome (<106 bp).
The description of this genome (Pérez-Brocal et al., 2006) noted and discussed this frameshift, suggesting confidence in the gene sequence; any of the other frameshifts could instead be sequencing errors.