The frontier between cell and organelle: genome analysis of Candidatus Carsonella ruddii

Tamames, Javier; Gil, Rosario; Latorre, Amparo; Peretó, Juli; Silva, Francisco J; Moya, Andrés

doi:10.1186/1471-2148-7-181

BMC Ecology and Evolution

Table 1 Essential genes involved in informational processes that are missing or degraded in C. ruddii genome.

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
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
DNA replication	DNA polymerase III, d subunit	holA	Absent
DNA replication	DNA polymerase III, d' subunit	holB	Absent
DNA replication	DNA polymerase III, g and t subunits	dnaX	Absent
DNA replication	DNA gyrase, A subunit	gyrA	Absent
DNA replication	DNA gyrase, B subunit	gyrB	Absent
DNA replication	DNA ligase	lig	Absent
DNA replication	single-strand DNA-binding protein	ssb	Absent
DNA repair, restriction, and modification	exonuclease	polA*	Absent
DNA repair, restriction, and modification	uracil-DNA glycosylase	ung	Absent
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
Transcription	transcription elongation factor	greA	Absent
Transcription	transcription pausing; L factor	nusA	Absent
Transcription	transcription antitermination protein	nusG	Absent
Aminoacyl-tRNA synthetase	arginyl-tRNA synthetase	argS	Absent
Aminoacyl-tRNA synthetase	asparaginyl-tRNA synthetase	asnS	Absent
Aminoacyl-tRNA synthetase	cysteinyl-tRNA synthetase	cysS	Absent
Aminoacyl-tRNA synthetase	glycyl-tRNA synthetase, β subunit	glyS	Absent
Aminoacyl-tRNA synthetase	histidyl-tRNA synthetase	hisS	Absent
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
Aminoacyl-tRNA synthetase	prolyl-tRNA synthetase	proS	Absent
Aminoacyl-tRNA synthetase	threonyl-tRNA synthetase	thrS	Absent
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
tRNA maduration and modification	peptidyl-tRNA hydrolase	pth	Absent
tRNA maduration and modification	protein component of ribonuclease P	rnpA	Absent
Ribosomal protein	50S ribosomal protein L3	rplC	Degraded	Loss of first half of the protein
Ribosomal protein	50S ribosomal protein L9	rplI	Absent
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
Ribosomal protein	50S ribosomal protein L23	rplW	Absent
Ribosomal protein	50S ribosomal protein L24	rplX	Absent
Ribosomal protein	50S ribosomal protein L29	rpmC	Absent
Ribosomal protein	50S ribosomal protein L34	rpmH	Absent
Ribosomal protein	50S ribosomal protein L35	rpmI	Absent
Ribosomal protein	30S ribosomal protein S6	rpsF	Absent
Ribosomal protein	30S ribosomal protein S18	rpsR	Absent
Ribosomal protein	30S ribosomal protein S20	rpsT	Absent
Ribosome function	GTP-binding protein	era	Absent
Ribosome function	ribosomal methytransferase	cspR	Absent
Ribosome function	dimethyladenosine transferase	ksgA	Absent
Ribosome function	ribosome-binding factor A	rbfA	Absent
Ribosome function	GTP-binding protein	ychF	Absent
Ribosome function	GTP-binding protein	engA	Absent
Ribosome function	GTP-binding protein, Obg family	obg (yhbZ)	Degraded	GTP binding sites are lost
Translation factors	elongation factor P	efp	Absent
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
Translation factors	GTP-binding elongation factor	lepA	Absent
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
RNA degradation	ribonuclease III	rnc	Absent

* The gene name corresponds to the one selected in the proposed minimal genome [13]. Although there are other genes for the same function in γ-proteobacteria, none of them is present in C. ruddii.

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ISSN: 2730-7182

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