The ins and outs of metal homeostasis by the root nodule actinobacterium Frankia

BMC Genomics

Table 1 Predicted number of metalloproteins in Frankia and other bacteria

Metal	[Dom #]	CcI3	ACN	QA3	EAN1	EUN	EuI1	CN3	DC12	B sub	C met	E col	H pyl	M tub
Co	[6]	7	13	12	9	13	15	15	11	11	26	13	6	8
Cu	[31]	27	28	34	36	41	31	42	29	23	72	17	6	16
Fe	[174]	245	279	328	400	457	445	514	275	179	398	227	77	188
Mo	[15]	7	18	15	18	20	16	20	11	8	28	24	2	12
Mn	[54]	74	102	117	156	144	167	185	91	72	102	76	25	99
Ni	[17]	25	35	39	38	32	30	28	24	13	29	20	14	14
Zn	[230]	174	279	336	388	401	422	483	264	156	305	168	58	215
Genome a		4621	6723	6546	7250	7833	7262	8412	5933	4354	6430	4427	1749	4062
% MPs		12.1	11.2	13.5	14.4	14.1	15.5	15.3	11.9	10.6	14.9	12.3	10.7	13.6
% MR		1.06	1.06	1.06	1.06	1.06	1.06	1.06	1.06	1.06	1.06	1.06	1.06	1.06

Proteins with metal ion binding properties were identified using Gene Ontology function search through the Joint Genome Institute – Integrated Microbial Genomes website (https://img.jgi.doe.gov). Identified protein domains for the metalloproteins were used to find orthologs in Frankia and other bacteria including: Bacillus subtilis subtilis 168 (B sub), Cupriavidus metallidurans CH34 (C met), Escherichia coli K12- W3110 (E col), Helicobacter pylori B8 (H pyl), Mycobacterium tuberculosis H37Rv (M tub), and Streptomyces viridochromogenes DSM 40736 (S vir). Genomes with significant (>1 S.D. from average) metalloprotein content, normalized to the genome size, are in bold. % MPs = percentage of total metalloproteins in the genome. %MR = percent metal resistance genes (binding, detoxification, and export) in the genome. [Dom #] = Number of unique protein families (pfam) or ortholog clusters (COG) that bind the indicated metal.
a. Total number of protein coding genes in each genome.

ISSN: 1471-2164