. 2024 Aug 21;9(9):e00422-24. doi: 10.1128/msystems.00422-24

TABLE 3.

Genes required for root attachment at pH 7.0 grouped by their requirement at different stages (rhizosphere, root colonization, nodule bacteria, and bacteroids) of nodule development

Gene	Name	Description	pH at which gene is required for attachment
Attachment specific (not required at any other stage)
pRL100112		Putative dehalogenase-hydrolase (HAD)	pH 7.0
pRL100174		Conserved hypothetical protein	pH 6.5, 7.0, and 7.5
pRL110043		Putative transmembrane arabinose efflux permease transporter protein	pH 6.5 and 7.0
RL0551	hslO	Hsp33-like chaperonin HslO	pH 6.5, 7.0, and 7.5
RL0617		Putative dTTP/UTP pyrophosphatase	pH 7.0 and 7.5
RL0876		Conserved hypothetical cytoplasmic protein	pH 6.5, 7.0, and 7.5
RL1052		Uncharacterized protein. Unknown localization	pH 7.0
RL1106^a	pspA	Putative PspA (phage shock protein A) family regulator	pH 7.0
RL1381		Uncharacterized protein. Unknown localization	pH 6.5, 7.0, and 7.5
RL1504		Uncharacterized cytoplasmic protein, NYN domain. Possibly novel RNAse with regulatory role	pH 7.0 and 7.5
RL1661^b	gmsA	Glucomannan biosynthesis protein GmsA	pH 6.5 and 7.0
RL2044	scpA	Segregation and condensation protein A participates in chromosomal division	pH 7.0
RL2513	tpiA	Putative triosephosphate isomerase TpiA	pH 6.5, 7.0, and 7.5
RL2520		Permease, transmembrane protein	pH 6.5 and 7.0
RL2587	anmK	Anhydro-N-acetylmuramic acid kinase AnmK. Required for cell wall recycling	pH 7.0
RL2695^a		Hypothetical protein (contiguous with RL2694 (gor) which is rhizosphere-progressive)	pH 7.0
RL3226	ahpD	Alkyl hydroperoxide reductase AhpD	pH 7.0
RL3277		Putative transmembrane DedA family protein	pH 6.5 and 7.0
RL3752^b	pssA	Glycosyl transferase involved in EPS biosynthesis	pH 6.5, 7.0, and 7.5
RL4083		Uncharacterized protein, SGHN family esterase domain. Unknown localization	pH 7.0 and 7.5
RL4145^b^,c	pckR	LacI family transcriptional regulator. Cytoplasmic protein.	pH 6.5, 7.0, and 7.5
RL4335		Uncharacterized protein	pH 6.5 and 7.0
RL4381		Putative POTRA-domain transporter	pH 6.5, 7.0, and 7.5
RL4382^b		Filamentous hemagglutinin adhesin	pH 6.5, 7.0, and 7.5
RL4704		Putative glyoxylase family protein, member of the VOC superfamily	pH 7.0
Required in attachment and rhizosphere only
RL2284	hfq	RNA-binding protein Hfq. Global post-transcriptional regulator	pH 6.5 & 7.0
RL4065^a^,d		Hypothetical cytoplasmic protein with no conserved domains	pH 6.5, 7.0, and 7.5
Required in attachment and root colonization only
pRL100242		Uncharacterized cytoplasmic protein	pH 6.5 and 7.0
RL1371^a		Putative transmembrane protein	pH 7.0
Attachment-progressive
pRL100053^b^,e		Putative transmembrane protein with helix-turn-helix 37 domain	pH 6.5, 7.0, and 7.5
RL1478	amn	AMP nucleosidase; catalyzes hydrolysis of AMP to form adenine and ribose 5-phosphate	pH 6.5, 7.0, and 7.5
RL3987^a	vapB	SpoVT-AbrB domain-containing protein. Antitoxin (VapB) of VapBC TA	pH 6.5, 7.0, and 7.5
Rhizosphere-progressive (required at every stage)
RL0052		Uncharacterized protein. Unknown localization	pH 7.0
RL1600	ppx	Putative exopolyphosphatase Ppx. Hydrolysis of EPS	pH 6.5 and 7.0
RL2694	gor	Glutathione reductase Gor (contiguous with RL2695 which is attachment-specific)	pH 7.0
RL3988	vapC	PIN domain-containing protein. Single-stranded RNA nuclease. Toxin (VapC) of VapBC TA	pH 6.5, 7.0, and 7.5
RL3989	ruvA	Holliday junction ATP-dependent DNA helicase RuvA	pH 6.5, 7.0, and 7.5
RL3990	ruvB	Holliday junction ATP-dependent DNA helicase RuvB	pH 6.5, 7.0, and 7.5
Required in attachment, nodule bacteria, and bacteroids
pRL120518^c		Putative TetR family transcriptional regulator	pH 7.0
RL0141	cycM	Membrane-bound cytochrome c CycM	pH 7.0 and 7.5
RL2212	clpS	ATP-dependent Clp protease adaptor protein ClpS	pH 7.0 and 7.5
RL2588	tyrS	Tyrosine-tRNA ligase TyrS. Catalyzes attachment of tyrosine to tRNA	pH 7.0
RL2637	recA	DNA repair and SOS response RecA	pH 6.5, 7.0, and 7.5
RL4309		Putative transmembrane DedA family protein	pH 6.5 and 7.0
RL4362^a		Putative cobalamin (vitamin B12) synthesis protein, CobW domain	pH 6.5, 7.0, and 7.5
RL4363	dacC	Putative penicillin-binding protein, peptidase S11 domain	pH 6.5, 7.0, and 7.5
Required in attachment and nodule bacteria only
pRL100220		Uncharacterized protein	pH 6.5 and 7.0
RL1013		Uncharacterized protein, 17 kDa Anti 2 motif. Unknown localization	pH 7.0
RL2227		Zinc metalloprotease. Potential role in membrane lipid processing	pH 6.5 and 7.0
RL2643	dksA2	Putative DnaK suppressor protein DksA2. Modulates RNA polymerase activity. Cytoplasmic	pH 7.0 and 7.5
RL3322	pfp	Putative pyrophosphate-fructose 6-phosphate 1-phosphotransferase	pH 6.5, 7.0, and 7.5
RL3766^a	rpoH1	RNA polymerase sigma-32-factor, heat shock sigma factor RpoH1	pH 6.5, 7.0, and 7.5
Required in attachment and advantaged when mutated in nodule bacteria
RL2400^a^,f		Putative MarC family transmembrane protein, unknown function	pH 6.5, 7.0, and 7.5
RL2642^a		Uncharacterized protein	pH 7.0 and 7.5

^{^a}

Gene contains fewer than 6 TA sites (eight genes).

^{^b}

Mutant made and assessed in Lux-based assay (five genes).

^{^c}

Gene encodes a regulator of gene expression (two genes).

^{^d}

Gene is also required in root colonization (one gene).

^{^e}

Mutant shown to have reduced root colonization (5 dpi) (26) (one gene)

^{^f}

Gene is also required in bacteroids (one gene).