Structural classification of bacterial response regulators: diversity of output domains and domain combinations

Abstract

CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. In this work, 4,610 response regulators, encoded in complete genomes of 200 bacterial and archaeal species, were identified and classified by their domain architectures. Previously uncharacterized output domains were analyzed and, in some cases, assigned to known domain families. Transcriptional regulators of the OmpR, NarL, and NtrC families were found to comprise almost 60% of all response regulators; transcriptional regulators with other DNA-binding domains (LytTR, AraC, Spo0A, Fis, YcbB, RpoE, and MerR) account for an additional 6%. The remaining one-third is represented by the stand-alone REC domain (approximately 14%) and its combinations with a variety of enzymatic (GGDEF, EAL, HD-GYP, CheB, CheC, PP2C, and HisK), RNA-binding (ANTAR and CsrA), protein- or ligand-binding (PAS, GAF, TPR, CAP_ED, and HPt) domains, or newly described domains of unknown function. The diversity of domain architectures and the abundance of alternative domain combinations suggest that fusions between the REC domain and various output domains is a widespread evolutionary mechanism that allows bacterial cells to regulate transcription, enzyme activity, and/or protein-protein interactions in response to environmental challenges. The complete list of response regulators encoded in each of the 200 analyzed genomes is available online at http://www.ncbi.nlm.nih.gov/Complete_Genomes/RRcensus.html.

FIG. 1.

Domain architectures of the most common types of bacterial response regulators. The sectors in the chart indicate the respective share of each domain combination and are colored similarly to the corresponding output domains. The sector marked as REC-Fis REC-AraC represents all rare DNA-binding response regulators listed in Table 2.

FIG. 2.

Domain architectures of response regulators with the histidine kinase (HisK) output domain. Domain symbols are drawn approximately to scale. Some of the domains are highly diverged and could be recognized only by searching the CDD database using relaxed stringency parameters. Source organisms, gene names, and NCBI protein database accession numbers for the domain architectures shown above are as follows (domain architecture number and accession number) B. subtilis ywpD (1; CAB05945) or Nostoc sp. PCC 7120 all3764 (1; BAB75463); Nostoc sp. PCC 7120 all1279 (2; BAB73236), alr1968 (16; BAB73667), and all4097 (17; BAB75796); Bradyrhizobium japonicum bll1030 (3; BAC46295); Haloarcula marismortui rrnAC0574 (4; AAV45588), rrnAC3379 (5; AAV48063), rrnAC2533 (6; AAV47335), rrnAC0075 (7; AAV45155), rrnAC0848 (8; AAV45829), rrnAC1626 (9; AAV46539), rrnAC3361 (10; AAV48050), rrnAC1495 (12; AAV46418), and pNG7156 (13; AAV44864); Synechocystis sp. PCC 6803 slr0222 (11; BAA10222); Anabaena variabilis Ava_B0191 (14; ABA24903); Gloeobacter violaceus gll0634 (15; BAC88575); Desulfovibrio vulgaris DVU2677 (18; AAS97149); Dechloromonas aromatica Daro_2847 (19; AAZ47577). Proteins with domain architecture numbers 1, 14, and 18 were considered bona fide response regulators.

FIG. 3.

Multiple sequence alignment of the Hnr-type output domain and its comparison with the protein phosphatase domains of the PP2C family. The top sequence is that of E. coli protein RssB (GenBank accession no. AAC74317). Conserved hydrophobic amino acid residues are shaded yellow; other conserved residues are shown in bold typeface. Metal-binding residues of PP2C-type protein phosphatases are shown in white letters on dark background. The numbers show the positions of aligned residues and the lengths of gaps between them. The numbers in parentheses signify the total length of each protein. The overlap between the secondary structure prediction by PSIPRED (59) and the known structures of PP2C-type protein phosphatases (32, 104) are shown above the alignment; cylinders indicate the α-helices, and arrows indicate the β-strands.

FIG. 4.

Correlation between the genome size and total number of encoded response regulators. Each symbol indicates the logarithm of the number of response regulators encoded in a single bacterial genome with the following color scheme: actinobacteria, black circles; cyanobacteria, cyan circles; alpha-proteobacteria, brown diamonds; beta-, delta-, and epsilon-proteobacteria, yellow diamonds; gamma-proteobacteria, blue squares; firmicutes, open squares; members of other bacterial phyla (Aquificales, Bacteroidetes, Chlamydiae, Deinococcus-Thermus, Planctomycetes, Spirochetes, and Thermotogales), red triangles. Archaeal response regulators are indicated by yellow triangles. Organisms that encode no response regulators are indicated by symbols on the x axis (logN = 0); these, however, were ignored for the calculation of the slope and the correlation coefficient of the regression line. The numbers in the circles indicate the data points corresponding to the following organisms: 1, Dechloromonas aromatica; 2, Geobacter sulfurreducens; 3, Wolinella succinogenes; 4, Dehalococcoides sp. strain CBDB1; 5, Sulfolobus solfataricus.