From: The frontier between cell and organelle: genome analysis of Candidatus Carsonella ruddii
Functional category | Product | Gene | Status | Comments |
---|---|---|---|---|
Chromosome-associated protein | DNA-binding protein | hupA* | Absent | Â |
DNA replication | replicative DNA helicase | dnaB | Degraded | Helicase domain is very degraded |
DNA replication | DNA primase | dnaG | Degraded | Helicase-binding domain and part of DNA-binding domain are missing |
DNA replication | DNA polymerase III, b subunit | dnaN | Absent | Â |
DNA replication | DNA polymerase III, d subunit | holA | Absent | Â |
DNA replication | DNA polymerase III, d' subunit | holB | Absent | Â |
DNA replication | DNA polymerase III, g and t subunits | dnaX | Absent | Â |
DNA replication | DNA gyrase, A subunit | gyrA | Absent | Â |
DNA replication | DNA gyrase, B subunit | gyrB | Absent | Â |
DNA replication | DNA ligase | lig | Absent | Â |
DNA replication | single-strand DNA-binding protein | ssb | Absent | Â |
DNA repair, restriction, and modification | exonuclease | polA* | Absent | Â |
DNA repair, restriction, and modification | uracil-DNA glycosylase | ung | Absent | Â |
Transcription | RNA polymerase major sigma factor | rpoD | Degraded | Three out of six domains of the protein have been lost. Other two are very degraded, including those responsible to bind both to -10 promoter region and RNA polymerase. |
Transcription | ATP-dependent RNA helicase | deaD | Absent | Â |
Transcription | transcription elongation factor | greA | Absent | Â |
Transcription | transcription pausing; L factor | nusA | Absent | Â |
Transcription | transcription antitermination protein | nusG | Absent | Â |
Aminoacyl-tRNA synthetase | arginyl-tRNA synthetase | argS | Absent | Â |
Aminoacyl-tRNA synthetase | asparaginyl-tRNA synthetase | asnS | Absent | Â |
Aminoacyl-tRNA synthetase | cysteinyl-tRNA synthetase | cysS | Absent | Â |
Aminoacyl-tRNA synthetase | glycyl-tRNA synthetase, β subunit | glyS | Absent |  |
Aminoacyl-tRNA synthetase | histidyl-tRNA synthetase | hisS | Absent | Â |
Aminoacyl-tRNA synthetase | phenylalanyl-tRNA synthetase, a subunit | pheS | Degraded | Aminoacyl tRNA synthetase class II N-terminal domain, and part of tRNA synthetases class II core domain are missing |
Aminoacyl-tRNA synthetase | phenylalanyl-tRNA synthetase, b subunit | pheT | Absent | Â |
Aminoacyl-tRNA synthetase | prolyl-tRNA synthetase | proS | Absent | Â |
Aminoacyl-tRNA synthetase | threonyl-tRNA synthetase | thrS | Absent | Â |
Aminoacyl-tRNA synthetase | valyl-tRNA synthetase | valS | Degraded | Most of the anticodon domain is missing. Mutations in functional residues |
tRNA maduration and modification | tRNA(Ile)-lysidine synthetase | mesJ | Absent | Â |
tRNA maduration and modification | peptidyl-tRNA hydrolase | pth | Absent | Â |
tRNA maduration and modification | protein component of ribonuclease P | rnpA | Absent | Â |
Ribosomal protein | 50S ribosomal protein L3 | rplC | Degraded | Loss of first half of the protein |
Ribosomal protein | 50S ribosomal protein L9 | rplI | Absent | Â |
Ribosomal protein | 50S ribosomal protein L13 | rplM | Degraded | Not matching family profile. Well conserved zones are mutated |
Ribosomal protein | 50S ribosomal protein L19 | rplS | Absent | Â |
Ribosomal protein | 50S ribosomal protein L23 | rplW | Absent | Â |
Ribosomal protein | 50S ribosomal protein L24 | rplX | Absent | Â |
Ribosomal protein | 50S ribosomal protein L29 | rpmC | Absent | Â |
Ribosomal protein | 50S ribosomal protein L34 | rpmH | Absent | Â |
Ribosomal protein | 50S ribosomal protein L35 | rpmI | Absent | Â |
Ribosomal protein | 30S ribosomal protein S6 | rpsF | Absent | Â |
Ribosomal protein | 30S ribosomal protein S18 | rpsR | Absent | Â |
Ribosomal protein | 30S ribosomal protein S20 | rpsT | Absent | Â |
Ribosome function | GTP-binding protein | era | Absent | Â |
Ribosome function | ribosomal methytransferase | cspR | Absent | Â |
Ribosome function | dimethyladenosine transferase | ksgA | Absent | Â |
Ribosome function | ribosome-binding factor A | rbfA | Absent | Â |
Ribosome function | GTP-binding protein | ychF | Absent | Â |
Ribosome function | GTP-binding protein | engA | Absent | Â |
Ribosome function | GTP-binding protein, Obg family | obg (yhbZ) | Degraded | GTP binding sites are lost |
Translation factors | elongation factor P | efp | Absent | Â |
Translation factors | ribosome recycling factor | frr | Degraded | Mutations in residues interacting with the ribosome, known to abolish functionality |
Translation factors | N5-glutamine methyltransferase | hemK | Absent | Â |
Translation factors | GTP-binding elongation factor | lepA | Absent | Â |
Translation factors | tmRNA-binding protein | smpB | Degraded | Missing some β strands important for β-barrel structure. Mutations in zones interacting with RNA. |
Translation factors | elongation factor Ts. | tsf | Degraded | Mutations in D80-F81, interacting with Ef-Tu, known to abolish functionality |
RNA degradation | polyribonucleotide nucleotidyltransferase | pnp | Absent | Â |
RNA degradation | ribonuclease III | rnc | Absent | Â |