Systematic Dissection and Trajectory-Scanning Mutagenesis of the Molecular Interface That Ensures Specificity of Two-Component Signaling Pathways
Two-component signal transduction systems enable bacteria to sense and respond to a wide range of environmental stimuli. Sensor histidine kinases transmit signals to their cognate response regulators via phosphorylation. The faithful transmission of information through two-component pathways and the avoidance of unwanted cross-talk require exquisite specificity of histidine kinase-response regulator interactions to ensure that cells mount the appropriate response to external signals. To identify putative specificity-determining residues, we have analyzed amino acid coevolution in two-component proteins and identified a set of residues that can be used to rationally rewire a model signaling pathway, EnvZ-OmpR. To explore how a relatively small set of residues can dictate partner selectivity, we combined alanine-scanning mutagenesis with an approach we call trajectory-scanning mutagenesis, in which all mutational intermediates between the specificity residues of EnvZ and another kinase, RstB, were systematically examined for phosphotransfer specificity. The same approach was used for the response regulators OmpR and RstA. Collectively, the results begin to reveal the molecular mechanism by which a small set of amino acids enables an individual kinase to discriminate amongst a large set of highly-related response regulators and vice versa. Our results also suggest that the mutational trajectories taken by two-component signaling proteins following gene or pathway duplication may be constrained and subject to differential selective pressures. Only some trajectories allow both the maintenance of phosphotransfer and the avoidance of unwanted cross-talk.
Vyšlo v časopise:
Systematic Dissection and Trajectory-Scanning Mutagenesis of the Molecular Interface That Ensures Specificity of Two-Component Signaling Pathways. PLoS Genet 6(11): e32767. doi:10.1371/journal.pgen.1001220
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1001220
Souhrn
Two-component signal transduction systems enable bacteria to sense and respond to a wide range of environmental stimuli. Sensor histidine kinases transmit signals to their cognate response regulators via phosphorylation. The faithful transmission of information through two-component pathways and the avoidance of unwanted cross-talk require exquisite specificity of histidine kinase-response regulator interactions to ensure that cells mount the appropriate response to external signals. To identify putative specificity-determining residues, we have analyzed amino acid coevolution in two-component proteins and identified a set of residues that can be used to rationally rewire a model signaling pathway, EnvZ-OmpR. To explore how a relatively small set of residues can dictate partner selectivity, we combined alanine-scanning mutagenesis with an approach we call trajectory-scanning mutagenesis, in which all mutational intermediates between the specificity residues of EnvZ and another kinase, RstB, were systematically examined for phosphotransfer specificity. The same approach was used for the response regulators OmpR and RstA. Collectively, the results begin to reveal the molecular mechanism by which a small set of amino acids enables an individual kinase to discriminate amongst a large set of highly-related response regulators and vice versa. Our results also suggest that the mutational trajectories taken by two-component signaling proteins following gene or pathway duplication may be constrained and subject to differential selective pressures. Only some trajectories allow both the maintenance of phosphotransfer and the avoidance of unwanted cross-talk.
Zdroje
1. SchwartzMA
MadhaniHD
2004 Principles of MAP kinase signaling specificity in Saccharomyces cerevisiae. Annu Rev Genet 38 725 748
2. UbersaxJA
FerrellJEJr
2007 Mechanisms of specificity in protein phosphorylation. Nat Rev Mol Cell Biol 8 530 541
3. StockAM
RobinsonVL
GoudreauPN
2000 Two-component signal transduction. Annu Rev Biochem 69 183 215
4. GaoR
MackTR
StockAM
2007 Bacterial response regulators: versatile regulatory strategies from common domains. Trends Biochem Sci 32 225 234
5. LaubMT
GoulianM
2007 Specificity in two-component signal transduction pathways. Annu Rev Genet 41 121 145
6. SkerkerJM
PrasolMS
PerchukBS
BiondiEG
LaubMT
2005 Two-component signal transduction pathways regulating growth and cell cycle progression in a bacterium: a system-level analysis. PLoS Biol 3 e334 doi:10.1371/journal.pbio.0030334
7. FisherSL
KimSK
WannerBL
WalshCT
1996 Kinetic comparison of the specificity of the vancomycin resistance VanS for two response regulators, VanR and PhoB. Biochemistry 35 4732 4740
8. GrimshawCE
HuangS
HansteinCG
StrauchMA
BurbulysD
1998 Synergistic kinetic interactions between components of the phosphorelay controlling sporulation in Bacillus subtilis. Biochemistry 37 1365 1375
9. SkerkerJM
PerchukBS
SiryapornA
LubinEA
AshenbergO
2008 Rewiring the specificity of two-component signal transduction systems. Cell 133 1043 1054
10. WeigtM
WhiteRA
SzurmantH
HochJA
HwaT
2009 Identification of direct residue contacts in protein-protein interaction by message passing. Proc Natl Acad Sci U S A 106 67 72
11. BurgerL
van NimwegenE
2008 Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method. Mol Syst Biol 4 165
12. WhiteRA
SzurmantH
HochJA
HwaT
2007 Features of protein-protein interactions in two-component signaling deduced from genomic libraries. Methods Enzymol 422 75 101
13. CasinoP
RubioV
MarinaA
2009 Structural insight into partner specificity and phosphoryl transfer in two-component signal transduction. Cell 139 325 336
14. GloorGB
MartinLC
WahlLM
DunnSD
2005 Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions. Biochemistry 44 7156 7165
15. QinL
CaiS
ZhuY
InouyeM
2003 Cysteine-scanning analysis of the dimerization domain of EnvZ, an osmosensing histidine kinase. J Bacteriol 185 3429 3435
16. OrtlundEA
BridghamJT
RedinboMR
ThorntonJW
2007 Crystal structure of an ancient protein: evolution by conformational epistasis. Science 317 1544 1548
17. CarlsonCD
WarrenCL
HauschildKE
OzersMS
QadirN
2010 Specificity landscapes of DNA binding molecules elucidate biological function. Proc Natl Acad Sci U S A 107 4544 4549
18. WeinreichDM
DelaneyNF
DepristoMA
HartlDL
2006 Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312 111 114
19. BridghamJT
OrtlundEA
ThorntonJW
2009 An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461 515 519
20. LunzerM
MillerSP
FelsheimR
DeanAM
2005 The biochemical architecture of an ancient adaptive landscape. Science 310 499 501
21. DorgaiL
YagilE
WeisbergRA
1995 Identifying determinants of recombination specificity: construction and characterization of mutant bacteriophage integrases. J Mol Biol 252 178 188
22. CunninghamBC
JhuraniP
NgP
WellsJA
1989 Receptor and antibody epitopes in human growth hormone identified by homolog-scanning mutagenesis. Science 243 1330 1336
23. MiyazakiK
ArnoldFH
1999 Exploring nonnatural evolutionary pathways by saturation mutagenesis: rapid improvement of protein function. J Mol Evol 49 716 720
24. BellCH
PorterSL
StrawsonA
StuartDI
ArmitageJP
2010 Using structural information to change the phosphotransfer specificity of a two-component chemotaxis signalling complex. PLoS Biol 8 e1000306 doi:10.1371/journal.pbio.1000306
25. HaldimannA
PrahaladMK
FisherSL
KimSK
WalshCT
1996 Altered recognition mutants of the response regulator PhoB: a new genetic strategy for studying protein-protein interactions. Proc Natl Acad Sci U S A 93 14361 14366
26. GrebeTW
StockJB
1999 The histidine protein kinase superfamily. Adv Microb Physiol 41 139 227
27. de HoonMJ
ImotoS
NolanJ
MiyanoS
2004 Open source clustering software. Bioinformatics 20 1453 1454
28. SaldanhaAJ
2004 Java Treeview—extensible visualization of microarray data. Bioinformatics 20 3246 3248
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2010 Číslo 11
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