TABLE 1

Domains identified in cytoplasmic chemoreceptorsa

Domain% (total no.) of chemoreceptors with domain located:No. of chemoreceptors of class IVa/class IVbTotal no. of proteinsDatabase
N-terminalC-terminal
PAS/PAC100 (367)0362/5367SMART
CZB0100 (114)17/97114PFAM
Protoglobin100 (104)010/22104PFAM
FIST100 (14)014/014SMART
GAF100 (14)014/014SMART
Cache_117 (2)83 (10)2/1012PFAM
Diacid_rec100 (9)01/89PFAM
SBP_bac_50100 (9)0/99PFAM
PilZ0100 (7)6/17PFAM
PBPb0100 (3)0/33SMART
Hemerythrin0100 (2)2/02PFAM
Fe_hyd_lg_C100 (2)02/02PFAM
HNOB100 (2)02/02PFAM
NMT10100 (1)1/01PFAM
CBS100 (1)01/01SMART
NIT100 (1)01/01PFAM
CHASE3100 (1)01/01PFAM
Bac_globin100 (1)01/01PFAM
DUF3365100 (1)01/01PFAM
  • a N-terminal indicates the percentage of chemoreceptors with the indicated domain found on the amino-terminal side of the MA domain, with the total number in parentheses. C-terminal indicates the percentage of chemoreceptors with the indicated domain found on the carboxy-terminal side of the MA domain, with the total number in parentheses. Class IVa chemoreceptors are cytoplasmic receptors with N-terminal domains that are 108 amino acids or longer, while class IVb chemoreceptors have N-terminal regions of <108 amino acids (7). “Database” indicates whether the domains were identified by using the SMART or PFAM database. The following domains were included in this table. PAS domain proteins interact with and respond to small molecules through bound cofactors, including FAD and heme groups (48). CZB domains bind zinc through conserved histidines and cysteines and in some cases are known to sense zinc, although this has not been confirmed for other CZB proteins (49, 50). PilZ domains bind and mediate a response to the secondary messenger c-di-GMP (77). Protoglobin domains coordinate a heme group and can respond to oxygen (78). FIST domains are proposed to bind small ligands, including amino acids (51). GAF domains interact with and respond to 3′,5′-cyclic GMP (cGMP) (53, 79). The Diacid_rec domain is proposed to bind and respond to carbohydrates (54). The PocR domain is a variant of the PAS domain and is predicted to bind hydrocarbons (55). Cache_1 and SBP_bac_5 domains are predicted to have a role in small-molecule recognition (56, 57). PBPb domains are high-affinity small-molecule binding domains characterized in ABC transporters (57). Hemerythrins bind and respond to oxygen through coordinated iron atoms (80, 81) and have also been reported to mediate responses to nitric oxide (82). NMT1 domains have been characterized for their role in the synthesis of the pyrimidine moiety of thiamine and are regulated by thiamine (83, 84). The HNOB domain coordinates heme and is predicted to interact with and respond to gaseous ligands, including nitric oxide (85). CBS domains bind and respond to molecules with adenosyl groups, such as AMP and ATP or S-adenosylmethionine (86). The NIT domain binds and responds to nitrate and nitrite (87). The CHASE3 domain has been characterized as an extracellular sensory domain, although the perceived ligand is unknown (88). The Bac_globin domain coordinates heme as a prosthetic group and binds oxygen reversibly (14, 89). DUF3365 domains are present in bacteria but are functionally uncharacterized.