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Comparative Study
. 2003 Dec;2(6):1151-61.
doi: 10.1128/EC.2.6.1151-1161.2003.

Whole-genome analysis of two-component signal transduction genes in fungal pathogens

Natalie L Catlett  1 , Olen C Yoder, B Gillian Turgeon
Affiliations
Comparative Study

Whole-genome analysis of two-component signal transduction genes in fungal pathogens

Natalie L Catlett et al. Eukaryot Cell. 2003 Dec.

Abstract

Two-component phosphorelay systems are minimally comprised of a histidine kinase (HK) component, which autophosphorylates in response to an environmental stimulus, and a response regulator (RR) component, which transmits the signal, resulting in an output such as activation of transcription, or of a mitogen-activated protein kinase cascade. The genomes of the yeasts Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Candida albicans encode one, three, and three HKs, respectively. In contrast, the genome sequences of the filamentous ascomycetes Neurospora crassa, Cochliobolus heterostrophus (Bipolaris maydis), Gibberella moniliformis (Fusarium verticillioides), and Botryotinia fuckeliana (Botrytis cinerea) encode an extensive family of two-component signaling proteins. The putative HKs fall into 11 classes. Most of these classes are represented in each filamentous ascomycete species examined. A few of these classes are significantly more prevalent in the fungal pathogens than in the saprobe N. crassa, suggesting that these groups contain paralogs required for virulence. Despite the larger numbers of HKs in filamentous ascomycetes than in yeasts, all of the ascomycetes contain virtually the same downstream histidine phosphotransfer proteins and RR proteins, suggesting extensive cross talk or redundancy among HKs.

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Figures

FIG. 1.
FIG. 1.
General schematic diagram of phosphorelay signaling (adapted from reference 57). An external signal is sensed by the sensor domain and triggers phosphorylation of a conserved histidine residue (H). This phosphate is transferred to a conserved aspartic acid residue (D) in the RR receiver domain, activating the effector domain to result in an output such as activation of transcription or a MAP kinase (MAPK) cascade. For a simple two-component system (top), the HK (sensor, phosphoacceptor, and ATP-binding domains) and the RR are separate proteins. A hybrid HK protein (bottom) contains both HK and RR domains and generally requires additional rounds of phosphorelay through an HPt domain and a second RR protein. The HPt domain can be part of the hybrid HK protein or a separate protein. Most eukaryotic and all fungal HKs are hybrids.
FIG. 2.
FIG. 2.
Midpoint-rooted phylogram of fungal HKs. (A) Conserved phosphoacceptor (PFAM00512), ATP-binding (PFAM02518), and RR receiver (PFAM00072) domain amino acid sequences were aligned by using ClustalW. The phylogram was constructed by using parsimony (PAUP4.0b8). One of the two trees obtained is shown. N. crassa predicted protein sequences (pink) are identified by WICGR unique identifier numbers. C. heterostrophus (yellow, Ch), G. moniliformis (blue, Gm), and B. fuckeliana (green, Bf) sequences were obtained by homology and splice consensus-based manual predictions from TMRI fungal genome sequences. Other protein sequences are from GenBank. Percent confidence obtained by bootstrap analysis (1,000 repetitions, 10 stepwise additions each) is shown for branches with greater than 50% support. (B) Scaled cartoon of domain structure for a representative protein from each group. For group XI, some members have additional PAS/PAC domains or a less conserved GAF domain.
FIG. 2.
FIG. 2.
Midpoint-rooted phylogram of fungal HKs. (A) Conserved phosphoacceptor (PFAM00512), ATP-binding (PFAM02518), and RR receiver (PFAM00072) domain amino acid sequences were aligned by using ClustalW. The phylogram was constructed by using parsimony (PAUP4.0b8). One of the two trees obtained is shown. N. crassa predicted protein sequences (pink) are identified by WICGR unique identifier numbers. C. heterostrophus (yellow, Ch), G. moniliformis (blue, Gm), and B. fuckeliana (green, Bf) sequences were obtained by homology and splice consensus-based manual predictions from TMRI fungal genome sequences. Other protein sequences are from GenBank. Percent confidence obtained by bootstrap analysis (1,000 repetitions, 10 stepwise additions each) is shown for branches with greater than 50% support. (B) Scaled cartoon of domain structure for a representative protein from each group. For group XI, some members have additional PAS/PAC domains or a less conserved GAF domain.
FIG. 3.
FIG. 3.
Alignment of the H-box sequence containing the phosphoaccepting histidine. Subalignments of the H-box region (58) from the sequence alignment used for Fig. 2 are shown. For each group, the consensus sequences for N. crassa (Nc), G. moniliformis (Gm), B. fuckeliana (Bf), and C. heterostrophus (Ch) are shown in bold at the top. (A) Conserved HK groups. Lowercase letters indicate amino acid residues that are not absolutely conserved among orthologs in the four euascomycetes considered here. Sequences from other ascomycetes (underlined) or paralogs (italicized) are represented by dashes for consensus (conserved) residues or the appropriate amino acid. (B) Divergent HK groups. All sequences are shown, even when two or more paralogs have identical H-box sequences. Absolutely conserved residues are shaded black, and residues conserved in at least 50% of all sequences are shaded gray. Asterisks indicate positions of conserved histidine residues.
FIG. 4.
FIG. 4.
Phylogram of HHK1 and related protein sequences. T-Coffee was used to align the NCU01823.1, GmHHK1, ChHHK1, CaHK1, SpMAK2, and SpMAK3 full-length peptide sequences. The phylogram was constructed by using parsimony. SpMAK2 and SpMAK3 are drawn as outgroups on the basis of bootstrap analysis. Numbers indicate branch lengths. BcHHK1 was omitted from the analysis because of missing sequence information. A scaled cartoon of the domain structure is shown to the right of each sequence.
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