-
1
-
-
63749115101
-
Bacterial nucleotide-based second messengers
-
Pesavento C, Hengge R, (2009) Bacterial nucleotide-based second messengers. Curr Opin Microbiol 12: 170-176.
-
(2009)
Curr Opin Microbiol
, vol.12
, pp. 170-176
-
-
Pesavento, C.1
Hengge, R.2
-
2
-
-
78751695365
-
cAMP, c-di-GMP, c-di-AMP and now cGMP: bacteria use them all!
-
Gomelsky M, (2011) cAMP, c-di-GMP, c-di-AMP and now cGMP: bacteria use them all! Mol Microbiol 79: 562-565.
-
(2011)
Mol Microbiol
, vol.79
, pp. 562-565
-
-
Gomelsky, M.1
-
3
-
-
0034866076
-
Comparative genomics and evolution of genes encoding bacterial (p)ppGpp synthetases/hydrolases (the Rel, RelA and SpoT proteins)
-
Mittenhuber G, (2001) Comparative genomics and evolution of genes encoding bacterial (p)ppGpp synthetases/hydrolases (the Rel, RelA and SpoT proteins). J Mol Microbiol Biotechnol 3: 585-600.
-
(2001)
J Mol Microbiol Biotechnol
, vol.3
, pp. 585-600
-
-
Mittenhuber, G.1
-
4
-
-
0017413237
-
Anomalous synthesis of ppGpp in growing cells
-
Gallant J, Palmer L, Pao CC, (1977) Anomalous synthesis of ppGpp in growing cells. Cell 11: 181-185.
-
(1977)
Cell
, vol.11
, pp. 181-185
-
-
Gallant, J.1
Palmer, L.2
Pao, C.C.3
-
5
-
-
79961224232
-
Single-molecule investigations of the stringent response machinery in living bacterial cells
-
English BP, Hauryliuk V, Sanamrad A, Tankov S, Dekker NH, et al. (2011) Single-molecule investigations of the stringent response machinery in living bacterial cells. Proc Natl Acad Sci U S A.
-
(2011)
Proc Natl Acad Sci U S A
-
-
English, B.P.1
Hauryliuk, V.2
Sanamrad, A.3
Tankov, S.4
Dekker, N.H.5
-
6
-
-
0015239820
-
On the regulation of guanosine tetraphosphate levels in stringent and relaxed strains of Escherichia coli
-
Lazzarini RA, Cashel M, Gallant J, (1971) On the regulation of guanosine tetraphosphate levels in stringent and relaxed strains of Escherichia coli. J Biol Chem 246: 4381-4385.
-
(1971)
J Biol Chem
, vol.246
, pp. 4381-4385
-
-
Lazzarini, R.A.1
Cashel, M.2
Gallant, J.3
-
7
-
-
0027937371
-
Stringent control during carbon starvation of marine Vibrio sp. strain S14: molecular cloning, nucleotide sequence, and deletion of the relA gene
-
Flardh K, Axberg T, Albertson NH, Kjelleberg S, (1994) Stringent control during carbon starvation of marine Vibrio sp. strain S14: molecular cloning, nucleotide sequence, and deletion of the relA gene. J Bacteriol 176: 5949-5957.
-
(1994)
J Bacteriol
, vol.176
, pp. 5949-5957
-
-
Flardh, K.1
Axberg, T.2
Albertson, N.H.3
Kjelleberg, S.4
-
8
-
-
18444368425
-
Iron limitation induces SpoT-dependent accumulation of ppGpp in Escherichia coli
-
Vinella D, Albrecht C, Cashel M, D'Ari R, (2005) Iron limitation induces SpoT-dependent accumulation of ppGpp in Escherichia coli. Mol Microbiol 56: 958-970.
-
(2005)
Mol Microbiol
, vol.56
, pp. 958-970
-
-
Vinella, D.1
Albrecht, C.2
Cashel, M.3
D'Ari, R.4
-
9
-
-
33750479525
-
Acyl carrier protein/SpoT interaction, the switch linking SpoT-dependent stress response to fatty acid metabolism
-
Battesti A, Bouveret E, (2006) Acyl carrier protein/SpoT interaction, the switch linking SpoT-dependent stress response to fatty acid metabolism. Mol Microbiol 62: 1048-1063.
-
(2006)
Mol Microbiol
, vol.62
, pp. 1048-1063
-
-
Battesti, A.1
Bouveret, E.2
-
10
-
-
0029079412
-
Guanosine 3′,5′-bispyrophosphate (ppGpp) synthesis in cells of Escherichia coli starved for Pi
-
Spira B, Silberstein N, Yagil E, (1995) Guanosine 3′,5′-bispyrophosphate (ppGpp) synthesis in cells of Escherichia coli starved for Pi. J Bacteriol 177: 4053-4058.
-
(1995)
J Bacteriol
, vol.177
, pp. 4053-4058
-
-
Spira, B.1
Silberstein, N.2
Yagil, E.3
-
11
-
-
0007825206
-
Synthesis of guanosine tetra- and pentaphosphate requires the presence of a codon-specific, uncharged transfer ribonucleic acid in the acceptor site of ribosomes
-
Haseltine W, Block R, (1973) Synthesis of guanosine tetra- and pentaphosphate requires the presence of a codon-specific, uncharged transfer ribonucleic acid in the acceptor site of ribosomes. Proc Natl Acad Sci U S A 70: 1564-1568.
-
(1973)
Proc Natl Acad Sci U S A
, vol.70
, pp. 1564-1568
-
-
Haseltine, W.1
Block, R.2
-
13
-
-
0014478832
-
Two compounds implicated in the function of the RC gene of Escherichia coli
-
Cashel M, Gallant J, (1969) Two compounds implicated in the function of the RC gene of Escherichia coli. Nature 221: 838-841.
-
(1969)
Nature
, vol.221
, pp. 838-841
-
-
Cashel, M.1
Gallant, J.2
-
14
-
-
0015515019
-
MSI and MSII made on ribosome in idling step of protein synthesis
-
Haseltine WA, Block R, Gilbert W, Weber K, (1972) MSI and MSII made on ribosome in idling step of protein synthesis. Nature 238: 381-384.
-
(1972)
Nature
, vol.238
, pp. 381-384
-
-
Haseltine, W.A.1
Block, R.2
Gilbert, W.3
Weber, K.4
-
15
-
-
0021099181
-
Guanosine 5′-triphosphate, 3′-diphosphate 5′-phosphohydrolase. Purification and substrate specificity
-
Hara A, Sy J, (1983) Guanosine 5′-triphosphate, 3′-diphosphate 5′-phosphohydrolase. Purification and substrate specificity. J Biol Chem 258: 1678-1683.
-
(1983)
J Biol Chem
, vol.258
, pp. 1678-1683
-
-
Hara, A.1
Sy, J.2
-
16
-
-
0015752570
-
Role of guanine nucleotides in protein synthesis. Elongation factor G and guanosine 5′-triphosphate,3′-diphosphate
-
Hamel E, Cashel M, (1973) Role of guanine nucleotides in protein synthesis. Elongation factor G and guanosine 5′-triphosphate,3′-diphosphate. Proc Natl Acad Sci U S A 70: 3250-3254.
-
(1973)
Proc Natl Acad Sci U S A
, vol.70
, pp. 3250-3254
-
-
Hamel, E.1
Cashel, M.2
-
17
-
-
0016250916
-
Guanine nucleotides in protein synthesis. Utilization of pppGpp and dGTP by initiation factor 2 and elongation factor Tu
-
Hamel E, Cashel M, (1974) Guanine nucleotides in protein synthesis. Utilization of pppGpp and dGTP by initiation factor 2 and elongation factor Tu. Arch Biochem Biophys 162: 293-300.
-
(1974)
Arch Biochem Biophys
, vol.162
, pp. 293-300
-
-
Hamel, E.1
Cashel, M.2
-
18
-
-
0025992789
-
Residual guanosine 3′,5′-bispyrophosphate synthetic activity of relA null mutants can be eliminated by spoT null mutations
-
Xiao H, Kalman M, Ikehara K, Zemel S, Glaser G, et al. (1991) Residual guanosine 3′,5′-bispyrophosphate synthetic activity of relA null mutants can be eliminated by spoT null mutations. J Biol Chem 266: 5980-5990.
-
(1991)
J Biol Chem
, vol.266
, pp. 5980-5990
-
-
Xiao, H.1
Kalman, M.2
Ikehara, K.3
Zemel, S.4
Glaser, G.5
-
19
-
-
0018177416
-
Mechanism of the in vitro breakdown of guanosine 5′-diphosphate 3′-diphosphate in Escherichia coli
-
Heinemeyer EA, Richter D, (1978) Mechanism of the in vitro breakdown of guanosine 5′-diphosphate 3′-diphosphate in Escherichia coli. Proc Natl Acad Sci U S A 75: 4180-4183.
-
(1978)
Proc Natl Acad Sci U S A
, vol.75
, pp. 4180-4183
-
-
Heinemeyer, E.A.1
Richter, D.2
-
20
-
-
0032408864
-
The HD domain defines a new superfamily of metal-dependent phosphohydrolases
-
Aravind L, Koonin EV, (1998) The HD domain defines a new superfamily of metal-dependent phosphohydrolases. Trends Biochem Sci 23: 469-472.
-
(1998)
Trends Biochem Sci
, vol.23
, pp. 469-472
-
-
Aravind, L.1
Koonin, E.V.2
-
21
-
-
2942590392
-
Two relA/spoT homologous genes are involved in the morphological and physiological differentiation of Streptomyces clavuligerus
-
Jin W, Ryu YG, Kang SG, Kim SK, Saito N, et al. (2004) Two relA/spoT homologous genes are involved in the morphological and physiological differentiation of Streptomyces clavuligerus. Microbiology 150: 1485-1493.
-
(2004)
Microbiology
, vol.150
, pp. 1485-1493
-
-
Jin, W.1
Ryu, Y.G.2
Kang, S.G.3
Kim, S.K.4
Saito, N.5
-
22
-
-
17544367082
-
A relA/spoT homologous gene from Streptomyces coelicolor A3(2) controls antibiotic biosynthetic genes
-
Martinez-Costa OH, Arias P, Romero NM, Parro V, Mellado RP, et al. (1996) A relA/spoT homologous gene from Streptomyces coelicolor A3(2) controls antibiotic biosynthetic genes. J Biol Chem 271: 10627-10634.
-
(1996)
J Biol Chem
, vol.271
, pp. 10627-10634
-
-
Martinez-Costa, O.H.1
Arias, P.2
Romero, N.M.3
Parro, V.4
Mellado, R.P.5
-
23
-
-
0031829736
-
The relA/spoT-homologous gene in Streptomyces coelicolor encodes both ribosome-dependent (p)ppGpp-synthesizing and -degrading activities
-
Martinez-Costa OH, Fernandez-Moreno MA, Malpartida F, (1998) The relA/spoT-homologous gene in Streptomyces coelicolor encodes both ribosome-dependent (p)ppGpp-synthesizing and-degrading activities. J Bacteriol 180: 4123-4132.
-
(1998)
J Bacteriol
, vol.180
, pp. 4123-4132
-
-
Martinez-Costa, O.H.1
Fernandez-Moreno, M.A.2
Malpartida, F.3
-
24
-
-
36849001752
-
A charge reversal differentiates (p)ppGpp synthesis by monofunctional and bifunctional Rel proteins
-
Sajish M, Tiwari D, Rananaware D, Nandicoori VK, Prakash B, (2007) A charge reversal differentiates (p)ppGpp synthesis by monofunctional and bifunctional Rel proteins. J Biol Chem 282: 34977-34983.
-
(2007)
J Biol Chem
, vol.282
, pp. 34977-34983
-
-
Sajish, M.1
Tiwari, D.2
Rananaware, D.3
Nandicoori, V.K.4
Prakash, B.5
-
25
-
-
0035036356
-
Functional analysis of relA and rshA, two relA/spoT homologues of Streptomyces coelicolor A3(2)
-
Sun J, Hesketh A, Bibb M, (2001) Functional analysis of relA and rshA, two relA/spoT homologues of Streptomyces coelicolor A3(2). J Bacteriol 183: 3488-3498.
-
(2001)
J Bacteriol
, vol.183
, pp. 3488-3498
-
-
Sun, J.1
Hesketh, A.2
Bibb, M.3
-
26
-
-
79955026314
-
The complex logic of stringent response regulation in Caulobacter crescentus: starvation signalling in an oligotrophic environment
-
Boutte CC, Crosson S, (2011) The complex logic of stringent response regulation in Caulobacter crescentus: starvation signalling in an oligotrophic environment. Mol Microbiol 80: 695-714.
-
(2011)
Mol Microbiol
, vol.80
, pp. 695-714
-
-
Boutte, C.C.1
Crosson, S.2
-
27
-
-
37348999598
-
Identification and functional analysis of novel (p)ppGpp synthetase genes in Bacillus subtilis
-
Nanamiya H, Kasai K, Nozawa A, Yun C-S, Narisawa T, et al. (2008) Identification and functional analysis of novel (p)ppGpp synthetase genes in Bacillus subtilis. Mol Microbiol 67: 291-304.
-
(2008)
Mol Microbiol
, vol.67
, pp. 291-304
-
-
Nanamiya, H.1
Kasai, K.2
Nozawa, A.3
Yun, C.-S.4
Narisawa, T.5
-
28
-
-
34548303811
-
Three gene products govern (p)ppGpp production by Streptococcus mutans
-
Lemos JA, Lin VK, Nascimento MM, Abranches J, Burne RA, (2007) Three gene products govern (p)ppGpp production by Streptococcus mutans. Mol Microbiol 65: 1568-1581.
-
(2007)
Mol Microbiol
, vol.65
, pp. 1568-1581
-
-
Lemos, J.A.1
Lin, V.K.2
Nascimento, M.M.3
Abranches, J.4
Burne, R.A.5
-
29
-
-
64149130399
-
Stringent response in Vibrio cholerae: genetic analysis of spoT gene function and identification of a novel (p)ppGpp synthetase gene
-
Das B, Pal RR, Bag S, Bhadra RK, (2009) Stringent response in Vibrio cholerae: genetic analysis of spoT gene function and identification of a novel (p)ppGpp synthetase gene. Mol Microbiol 72: 380-398.
-
(2009)
Mol Microbiol
, vol.72
, pp. 380-398
-
-
Das, B.1
Pal, R.R.2
Bag, S.3
Bhadra, R.K.4
-
30
-
-
77957823929
-
A metazoan ortholog of SpoT hydrolyzes ppGpp and functions in starvation responses
-
Sun D, Lee G, Lee JH, Kim HY, Rhee HW, et al. (2010) A metazoan ortholog of SpoT hydrolyzes ppGpp and functions in starvation responses. Nat Struct Mol Biol 17: 1188-1194.
-
(2010)
Nat Struct Mol Biol
, vol.17
, pp. 1188-1194
-
-
Sun, D.1
Lee, G.2
Lee, J.H.3
Kim, H.Y.4
Rhee, H.W.5
-
31
-
-
79961029191
-
Signalling by the global regulatory molecule ppGpp in bacteria and chloroplasts of land plants
-
In Press
-
Tozawa Y, Nomura Y, (2011) Signalling by the global regulatory molecule ppGpp in bacteria and chloroplasts of land plants. Plant Biology In Press.
-
(2011)
Plant Biology
-
-
Tozawa, Y.1
Nomura, Y.2
-
32
-
-
40049090539
-
Still looking for the magic spot: the crystallographically defined binding site for ppGpp on RNA polymerase is unlikely to be responsible for rRNA transcription regulation
-
Vrentas CE, Gaal T, Berkmen MB, Rutherford ST, Haugen SP, et al. (2008) Still looking for the magic spot: the crystallographically defined binding site for ppGpp on RNA polymerase is unlikely to be responsible for rRNA transcription regulation. J Mol Biol 377: 551-564.
-
(2008)
J Mol Biol
, vol.377
, pp. 551-564
-
-
Vrentas, C.E.1
Gaal, T.2
Berkmen, M.B.3
Rutherford, S.T.4
Haugen, S.P.5
-
33
-
-
33749021074
-
The nucleotide-binding site of bacterial translation initiation factor 2 (IF2) as a metabolic sensor
-
Milon P, Tischenko E, Tomsic J, Caserta E, Folkers G, et al. (2006) The nucleotide-binding site of bacterial translation initiation factor 2 (IF2) as a metabolic sensor. Proc Natl Acad Sci U S A 103: 13962-13967.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 13962-13967
-
-
Milon, P.1
Tischenko, E.2
Tomsic, J.3
Caserta, E.4
Folkers, G.5
-
34
-
-
77957233585
-
Thermodynamic characterization of ppGpp binding to EF-G or IF2 and of initiator tRNA binding to free IF2 in the presence of GDP, GTP, or ppGpp
-
Mitkevich VA, Ermakov A, Kulikova AA, Tankov S, Shyp V, et al. (2010) Thermodynamic characterization of ppGpp binding to EF-G or IF2 and of initiator tRNA binding to free IF2 in the presence of GDP, GTP, or ppGpp. J Mol Biol 402: 838-846.
-
(2010)
J Mol Biol
, vol.402
, pp. 838-846
-
-
Mitkevich, V.A.1
Ermakov, A.2
Kulikova, A.A.3
Tankov, S.4
Shyp, V.5
-
35
-
-
79952280501
-
Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase
-
Kanjee U, Gutsche I, Alexopoulos E, Zhao B, El Bakkouri M, et al. (2011) Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase. EMBO J 30: 931-944.
-
(2011)
EMBO J
, vol.30
, pp. 931-944
-
-
Kanjee, U.1
Gutsche, I.2
Alexopoulos, E.3
Zhao, B.4
El Bakkouri, M.5
-
36
-
-
72649089509
-
ppGpp inhibits the activity of Escherichia coli DnaG primase
-
Maciag M, Kochanowska M, Lyzen R, Wegrzyn G, Szalewska-Palasz A, (2010) ppGpp inhibits the activity of Escherichia coli DnaG primase. Plasmid 63: 61-67.
-
(2010)
Plasmid
, vol.63
, pp. 61-67
-
-
Maciag, M.1
Kochanowska, M.2
Lyzen, R.3
Wegrzyn, G.4
Szalewska-Palasz, A.5
-
37
-
-
79551662182
-
ppGpp is the major source of growth rate control in E. coli
-
Potrykus K, Murphy H, Philippe N, Cashel M, (2011) ppGpp is the major source of growth rate control in E. coli. Environ Microbiol 13: 563-575.
-
(2011)
Environ Microbiol
, vol.13
, pp. 563-575
-
-
Potrykus, K.1
Murphy, H.2
Philippe, N.3
Cashel, M.4
-
38
-
-
42149158392
-
Control of bacterial transcription, translation and replication by (p)ppGpp
-
Srivatsan A, Wang JD, (2008) Control of bacterial transcription, translation and replication by (p)ppGpp. Curr Opin Microbiol 11: 100-105.
-
(2008)
Curr Opin Microbiol
, vol.11
, pp. 100-105
-
-
Srivatsan, A.1
Wang, J.D.2
-
39
-
-
77952902996
-
ppGpp conjures bacterial virulence
-
Dalebroux ZD, Svensson SL, Gaynor EC, Swanson MS, (2010) ppGpp conjures bacterial virulence. Microbiol Mol Biol Rev 74: 171-199.
-
(2010)
Microbiol Mol Biol Rev
, vol.74
, pp. 171-199
-
-
Dalebroux, Z.D.1
Svensson, S.L.2
Gaynor, E.C.3
Swanson, M.S.4
-
40
-
-
1842766260
-
Conformational antagonism between opposing active sites in a bifunctional RelA/SpoT homolog modulates (p)ppGpp metabolism during the stringent response [corrected]
-
Hogg T, Mechold U, Malke H, Cashel M, Hilgenfeld R, (2004) Conformational antagonism between opposing active sites in a bifunctional RelA/SpoT homolog modulates (p)ppGpp metabolism during the stringent response [corrected]. Cell 117: 57-68.
-
(2004)
Cell
, vol.117
, pp. 57-68
-
-
Hogg, T.1
Mechold, U.2
Malke, H.3
Cashel, M.4
Hilgenfeld, R.5
-
41
-
-
22744459778
-
Functional regulation of the opposing (p)ppGpp synthetase/hydrolase activities of RelMtb from Mycobacterium tuberculosis
-
Avarbock A, Avarbock D, Teh JS, Buckstein M, Wang ZM, et al. (2005) Functional regulation of the opposing (p)ppGpp synthetase/hydrolase activities of RelMtb from Mycobacterium tuberculosis. Biochemistry 44: 9913-9923.
-
(2005)
Biochemistry
, vol.44
, pp. 9913-9923
-
-
Avarbock, A.1
Avarbock, D.2
Teh, J.S.3
Buckstein, M.4
Wang, Z.M.5
-
42
-
-
0035150018
-
Regulation of Escherichia coli RelA requires oligomerization of the C-terminal domain
-
Gropp M, Strausz Y, Gross M, Glaser G, (2001) Regulation of Escherichia coli RelA requires oligomerization of the C-terminal domain. J Bacteriol 183: 570-579.
-
(2001)
J Bacteriol
, vol.183
, pp. 570-579
-
-
Gropp, M.1
Strausz, Y.2
Gross, M.3
Glaser, G.4
-
43
-
-
0036094741
-
Intramolecular regulation of the opposing (p)ppGpp catalytic activities of Rel(Seq), the Rel/Spo enzyme from Streptococcus equisimilis
-
Mechold U, Murphy H, Brown L, Cashel M, (2002) Intramolecular regulation of the opposing (p)ppGpp catalytic activities of Rel(Seq), the Rel/Spo enzyme from Streptococcus equisimilis. J Bacteriol 184: 2878-2888.
-
(2002)
J Bacteriol
, vol.184
, pp. 2878-2888
-
-
Mechold, U.1
Murphy, H.2
Brown, L.3
Cashel, M.4
-
44
-
-
66149086924
-
The significance of EXDD and RXKD motif conservation in Rel proteins
-
Sajish M, Kalayil S, Verma SK, Nandicoori VK, Prakash B, (2009) The significance of EXDD and RXKD motif conservation in Rel proteins. J Biol Chem 284: 9115-9123.
-
(2009)
J Biol Chem
, vol.284
, pp. 9115-9123
-
-
Sajish, M.1
Kalayil, S.2
Verma, S.K.3
Nandicoori, V.K.4
Prakash, B.5
-
45
-
-
33644876020
-
Pfam: clans, web tools and services
-
Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, et al. (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34: D247-251.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 247-251
-
-
Finn, R.D.1
Mistry, J.2
Schuster-Bockler, B.3
Griffiths-Jones, S.4
Hollich, V.5
-
46
-
-
13744252890
-
MAFFT version 5: improvement in accuracy of multiple sequence alignment
-
Katoh K, Kuma K, Toh H, Miyata T, (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33: 511-518.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.2
Toh, H.3
Miyata, T.4
-
47
-
-
33750403801
-
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
Stamatakis A, (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
-
(2006)
Bioinformatics
, vol.22
, pp. 2688-2690
-
-
Stamatakis, A.1
-
48
-
-
79952151614
-
Evolution of elongation factor G and the origins of mitochondrial and chloroplast forms
-
Atkinson GC, Baldauf SL, (2011) Evolution of elongation factor G and the origins of mitochondrial and chloroplast forms. Mol Biol Evol 28: 1281-1292.
-
(2011)
Mol Biol Evol
, vol.28
, pp. 1281-1292
-
-
Atkinson, G.C.1
Baldauf, S.L.2
-
49
-
-
0031743421
-
Profile hidden Markov models
-
Eddy SR, (1998) Profile hidden Markov models. Bioinformatics 14: 755-763.
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
-
50
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
Ronquist F, Huelsenbeck J, (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
-
(2003)
Bioinformatics
, vol.19
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.2
-
51
-
-
0035061686
-
Maximum-likelihood approach for gene family evolution under functional divergence
-
Gu X, (2001) Maximum-likelihood approach for gene family evolution under functional divergence. Mol Biol Evol 18: 453-464.
-
(2001)
Mol Biol Evol
, vol.18
, pp. 453-464
-
-
Gu, X.1
-
52
-
-
33748784344
-
A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences
-
Gu X, (2006) A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences. Mol Biol Evol 23: 1937-1945.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 1937-1945
-
-
Gu, X.1
-
53
-
-
0036205440
-
DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family
-
Gu X, Vander Velden K, (2002) DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family. Bioinformatics 18: 500-501.
-
(2002)
Bioinformatics
, vol.18
, pp. 500-501
-
-
Gu, X.1
Vander Velden, K.2
-
54
-
-
3242891318
-
The DISOPRED server for the prediction of protein disorder
-
Ward JJ, McGuffin LJ, Bryson K, Buxton BF, Jones DT, (2004) The DISOPRED server for the prediction of protein disorder. Bioinformatics 20: 2138-2139.
-
(2004)
Bioinformatics
, vol.20
, pp. 2138-2139
-
-
Ward, J.J.1
McGuffin, L.J.2
Bryson, K.3
Buxton, B.F.4
Jones, D.T.5
-
55
-
-
0034697980
-
Predicting subcellular localization of proteins based on their N-terminal amino acid sequence
-
Emanuelsson O, Nielsen H, Brunak S, von Heijne G, (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 300: 1005-1016.
-
(2000)
J Mol Biol
, vol.300
, pp. 1005-1016
-
-
Emanuelsson, O.1
Nielsen, H.2
Brunak, S.3
von Heijne, G.4
-
56
-
-
79954580509
-
The PyMOL Molecular Graphics System, Version 1.3r1
-
Schrodinger, LLC
-
Schrodinger, LLC (2010) The PyMOL Molecular Graphics System, Version 1.3r1.
-
(2010)
-
-
-
57
-
-
75749127849
-
The compartmentalized bacteria of the planctomycetes-verrucomicrobia-chlamydiae superphylum have membrane coat-like proteins
-
Santarella-Mellwig R, Franke J, Jaedicke A, Gorjanacz M, Bauer U, et al. (2010) The compartmentalized bacteria of the planctomycetes-verrucomicrobia-chlamydiae superphylum have membrane coat-like proteins. PLoS Biol 8: e1000281.
-
(2010)
PLoS Biol
, vol.8
-
-
Santarella-Mellwig, R.1
Franke, J.2
Jaedicke, A.3
Gorjanacz, M.4
Bauer, U.5
-
58
-
-
33744927902
-
The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance
-
Wagner M, Horn M, (2006) The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr Opin Biotechnol 17: 241-249.
-
(2006)
Curr Opin Biotechnol
, vol.17
, pp. 241-249
-
-
Wagner, M.1
Horn, M.2
-
59
-
-
33847189497
-
Synthesis and hydrolysis of pppGpp in mycobacteria: a ligand mediated conformational switch in Rel
-
Jain V, Saleem-Batcha R, Chatterji D, (2007) Synthesis and hydrolysis of pppGpp in mycobacteria: a ligand mediated conformational switch in Rel. Biophys Chem 127: 41-50.
-
(2007)
Biophys Chem
, vol.127
, pp. 41-50
-
-
Jain, V.1
Saleem-Batcha, R.2
Chatterji, D.3
-
60
-
-
77951062024
-
Phylogeny of gammaproteobacteria
-
Williams KP, Gillespie JJ, Sobral BW, Nordberg EK, Snyder EE, et al. (2010) Phylogeny of gammaproteobacteria. J Bacteriol 192: 2305-2314.
-
(2010)
J Bacteriol
, vol.192
, pp. 2305-2314
-
-
Williams, K.P.1
Gillespie, J.J.2
Sobral, B.W.3
Nordberg, E.K.4
Snyder, E.E.5
-
61
-
-
0031865507
-
Signature sequences in diverse proteins provide evidence of a close evolutionary relationship between the Deinococcus-thermus group and cyanobacteria
-
Gupta RS, Johari V, (1998) Signature sequences in diverse proteins provide evidence of a close evolutionary relationship between the Deinococcus-thermus group and cyanobacteria. J Mol Evol 46: 716-720.
-
(1998)
J Mol Evol
, vol.46
, pp. 716-720
-
-
Gupta, R.S.1
Johari, V.2
-
62
-
-
77349112000
-
The endosymbiotic origin, diversification and fate of plastids
-
Keeling PJ, (2010) The endosymbiotic origin, diversification and fate of plastids. Philos Trans R Soc Lond B Biol Sci 365: 729-748.
-
(2010)
Philos Trans R Soc Lond B Biol Sci
, vol.365
, pp. 729-748
-
-
Keeling, P.J.1
-
63
-
-
0034724194
-
Arabidopsis RelA/SpoT homologs implicate (p)ppGpp in plant signaling
-
van der Biezen EA, Sun J, Coleman MJ, Bibb MJ, Jones JD, (2000) Arabidopsis RelA/SpoT homologs implicate (p)ppGpp in plant signaling. Proc Natl Acad Sci U S A 97: 3747-3752.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 3747-3752
-
-
van der Biezen, E.A.1
Sun, J.2
Coleman, M.J.3
Bibb, M.J.4
Jones, J.D.5
-
64
-
-
79954532607
-
Rickettsial evolution in the light of comparative genomics
-
Merhej V, Raoult D, (2011) Rickettsial evolution in the light of comparative genomics. Biol Rev Camb Philos Soc 86: 379-405.
-
(2011)
Biol Rev Camb Philos Soc
, vol.86
, pp. 379-405
-
-
Merhej, V.1
Raoult, D.2
-
65
-
-
34249944112
-
The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes
-
Cho NH, Kim HR, Lee JH, Kim SY, Kim J, et al. (2007) The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes. Proc Natl Acad Sci U S A 104: 7981-7986.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 7981-7986
-
-
Cho, N.H.1
Kim, H.R.2
Lee, J.H.3
Kim, S.Y.4
Kim, J.5
-
66
-
-
23944507559
-
The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite
-
Ogata H, Renesto P, Audic S, Robert C, Blanc G, et al. (2005) The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite. PLoS Biol 3: e248.
-
(2005)
PLoS Biol
, vol.3
-
-
Ogata, H.1
Renesto, P.2
Audic, S.3
Robert, C.4
Blanc, G.5
-
67
-
-
14644404991
-
Transcriptional response of Rickettsia conorii exposed to temperature variation and stress starvation
-
Rovery C, Renesto P, Crapoulet N, Matsumoto K, Parola P, et al. (2005) Transcriptional response of Rickettsia conorii exposed to temperature variation and stress starvation. Res Microbiol 156: 211-218.
-
(2005)
Res Microbiol
, vol.156
, pp. 211-218
-
-
Rovery, C.1
Renesto, P.2
Crapoulet, N.3
Matsumoto, K.4
Parola, P.5
-
68
-
-
79953324145
-
Complementation of Rickettsia rickettsii RelA/SpoT Restores a Nonlytic Plaque Phenotype
-
Clark TR, Ellison DW, Kleba B, Hackstadt T, (2011) Complementation of Rickettsia rickettsii RelA/SpoT Restores a Nonlytic Plaque Phenotype. Infect Immun 79: 1631-1637.
-
(2011)
Infect Immun
, vol.79
, pp. 1631-1637
-
-
Clark, T.R.1
Ellison, D.W.2
Kleba, B.3
Hackstadt, T.4
-
69
-
-
34249079154
-
Network motifs: theory and experimental approaches
-
Alon U, (2007) Network motifs: theory and experimental approaches. Nat Rev Genet 8: 450-461.
-
(2007)
Nat Rev Genet
, vol.8
, pp. 450-461
-
-
Alon, U.1
-
70
-
-
70349979453
-
Phylogeny of prokaryotes: does it exist and why should we care?
-
Gribaldo S, Brochier C, (2009) Phylogeny of prokaryotes: does it exist and why should we care? Res Microbiol 160: 513-521.
-
(2009)
Res Microbiol
, vol.160
, pp. 513-521
-
-
Gribaldo, S.1
Brochier, C.2
-
71
-
-
78649395975
-
Evolution. Intermediate steps
-
Devos DP, Reynaud EG, (2010) Evolution. Intermediate steps. Science 330: 1187-1188.
-
(2010)
Science
, vol.330
, pp. 1187-1188
-
-
Devos, D.P.1
Reynaud, E.G.2
-
72
-
-
77956528790
-
Fundamental limits on the suppression of molecular fluctuations
-
Lestas I, Vinnicombe G, Paulsson J, (2010) Fundamental limits on the suppression of molecular fluctuations. Nature 467: 174-178.
-
(2010)
Nature
, vol.467
, pp. 174-178
-
-
Lestas, I.1
Vinnicombe, G.2
Paulsson, J.3
-
74
-
-
0030797355
-
Robustness in simple biochemical networks
-
Barkai N, Leibler S, (1997) Robustness in simple biochemical networks. Nature 387: 913-917.
-
(1997)
Nature
, vol.387
, pp. 913-917
-
-
Barkai, N.1
Leibler, S.2
-
75
-
-
77949398351
-
Structural sources of robustness in biochemical reaction networks
-
Shinar G, Feinberg M, (2010) Structural sources of robustness in biochemical reaction networks. Science 327: 1389-1391.
-
(2010)
Science
, vol.327
, pp. 1389-1391
-
-
Shinar, G.1
Feinberg, M.2
-
76
-
-
34547604468
-
Noise in gene expression determines cell fate in Bacillus subtilis
-
Maamar H, Raj A, Dubnau D, (2007) Noise in gene expression determines cell fate in Bacillus subtilis. Science 317: 526-529.
-
(2007)
Science
, vol.317
, pp. 526-529
-
-
Maamar, H.1
Raj, A.2
Dubnau, D.3
-
77
-
-
46349090277
-
Positive feedback and noise activate the stringent response regulator rel in mycobacteria
-
Sureka K, Ghosh B, Dasgupta A, Basu J, Kundu M, et al. (2008) Positive feedback and noise activate the stringent response regulator rel in mycobacteria. PLoS ONE 3: e1771.
-
(2008)
PLoS ONE
, vol.3
-
-
Sureka, K.1
Ghosh, B.2
Dasgupta, A.3
Basu, J.4
Kundu, M.5
-
78
-
-
0036684665
-
The role of the stringent response in the pathogenesis of bacterial infections
-
Godfrey HP, Bugrysheva JV, Cabello FC, (2002) The role of the stringent response in the pathogenesis of bacterial infections. Trends Microbiol 10: 349-351.
-
(2002)
Trends Microbiol
, vol.10
, pp. 349-351
-
-
Godfrey, H.P.1
Bugrysheva, J.V.2
Cabello, F.C.3
-
79
-
-
0043192889
-
The role of RelMtb-mediated adaptation to stationary phase in long-term persistence of Mycobacterium tuberculosis in mice
-
Dahl JL, Kraus CN, Boshoff HI, Doan B, Foley K, et al. (2003) The role of RelMtb-mediated adaptation to stationary phase in long-term persistence of Mycobacterium tuberculosis in mice. Proc Natl Acad Sci U S A 100: 10026-10031.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 10026-10031
-
-
Dahl, J.L.1
Kraus, C.N.2
Boshoff, H.I.3
Doan, B.4
Foley, K.5
-
80
-
-
0344826574
-
Characterization of the hipA7 allele of Escherichia coli and evidence that high persistence is governed by (p)ppGpp synthesis
-
Korch SB, Henderson TA, Hill TM, (2003) Characterization of the hipA7 allele of Escherichia coli and evidence that high persistence is governed by (p)ppGpp synthesis. Mol Microbiol 50: 1199-1213.
-
(2003)
Mol Microbiol
, vol.50
, pp. 1199-1213
-
-
Korch, S.B.1
Henderson, T.A.2
Hill, T.M.3
-
81
-
-
4644343922
-
Bacterial persistence as a phenotypic switch
-
Balaban NQ, Merrin J, Chait R, Kowalik L, Leibler S, (2004) Bacterial persistence as a phenotypic switch. Science 305: 1622-1625.
-
(2004)
Science
, vol.305
, pp. 1622-1625
-
-
Balaban, N.Q.1
Merrin, J.2
Chait, R.3
Kowalik, L.4
Leibler, S.5
-
82
-
-
79251586863
-
Phenotypic heterogeneity in mycobacterial stringent response
-
Ghosh S, Sureka K, Ghosh B, Bose I, Basu J, et al. (2011) Phenotypic heterogeneity in mycobacterial stringent response. BMC Syst Biol 5: 18.
-
(2011)
BMC Syst Biol
, vol.5
, pp. 18
-
-
Ghosh, S.1
Sureka, K.2
Ghosh, B.3
Bose, I.4
Basu, J.5
-
84
-
-
0033616714
-
Horizontal gene transfer among genomes: the complexity hypothesis
-
Jain R, Rivera M, Lake J, (1999) Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci U S A 96: 3801-3806.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 3801-3806
-
-
Jain, R.1
Rivera, M.2
Lake, J.3
-
85
-
-
77953115788
-
Cost of unneeded proteins in E. coli is reduced after several generations in exponential growth
-
Shachrai I, Zaslaver A, Alon U, Dekel E, (2010) Cost of unneeded proteins in E. coli is reduced after several generations in exponential growth. Mol Cell 38: 758-767.
-
(2010)
Mol Cell
, vol.38
, pp. 758-767
-
-
Shachrai, I.1
Zaslaver, A.2
Alon, U.3
Dekel, E.4
-
86
-
-
37249058775
-
Calcium-activated (p)ppGpp synthetase in chloroplasts of land plants
-
Tozawa Y, Nozawa A, Kanno T, Narisawa T, Masuda S, et al. (2007) Calcium-activated (p)ppGpp synthetase in chloroplasts of land plants. J Biol Chem 282: 35536-35545.
-
(2007)
J Biol Chem
, vol.282
, pp. 35536-35545
-
-
Tozawa, Y.1
Nozawa, A.2
Kanno, T.3
Narisawa, T.4
Masuda, S.5
-
87
-
-
47649104484
-
Horizontal gene transfer in eukaryotic evolution
-
Keeling PJ, Palmer JD, (2008) Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet 9: 605-618.
-
(2008)
Nat Rev Genet
, vol.9
, pp. 605-618
-
-
Keeling, P.J.1
Palmer, J.D.2
-
88
-
-
0042019958
-
cAMP signaling in Dictyostelium. Complexity of cAMP synthesis, degradation and detection
-
Saran S, Meima ME, Alvarez-Curto E, Weening KE, Rozen DE, et al. (2002) cAMP signaling in Dictyostelium. Complexity of cAMP synthesis, degradation and detection. J Muscle Res Cell Motil 23: 793-802.
-
(2002)
J Muscle Res Cell Motil
, vol.23
, pp. 793-802
-
-
Saran, S.1
Meima, M.E.2
Alvarez-Curto, E.3
Weening, K.E.4
Rozen, D.E.5
-
89
-
-
0018363503
-
The search for guanosine tetraphosphate (ppGpp) and other unusual nucleotides in eucaryotes
-
Silverman RH, Atherly AG, (1979) The search for guanosine tetraphosphate (ppGpp) and other unusual nucleotides in eucaryotes. Microbiol Rev 43: 27-41.
-
(1979)
Microbiol Rev
, vol.43
, pp. 27-41
-
-
Silverman, R.H.1
Atherly, A.G.2
-
90
-
-
67650136762
-
Degradation of ppGpp by nudix pyrophosphatase modulates the transition of growth phase in the bacterium Thermus thermophilus
-
Ooga T, Ohashi Y, Kuramitsu S, Koyama Y, Tomita M, et al. (2009) Degradation of ppGpp by nudix pyrophosphatase modulates the transition of growth phase in the bacterium Thermus thermophilus. J Biol Chem 284: 15549-15556.
-
(2009)
J Biol Chem
, vol.284
, pp. 15549-15556
-
-
Ooga, T.1
Ohashi, Y.2
Kuramitsu, S.3
Koyama, Y.4
Tomita, M.5
-
91
-
-
0016747976
-
Purine nucleotide pyrophosphotransferase from Streptomyces morookaensis, capable of synthesizing pppApp and pppGpp
-
Oki T, Yoshimoto A, Sato S, Takamatsu A, (1975) Purine nucleotide pyrophosphotransferase from Streptomyces morookaensis, capable of synthesizing pppApp and pppGpp. Biochim Biophys Acta 410: 262-272.
-
(1975)
Biochim Biophys Acta
, vol.410
, pp. 262-272
-
-
Oki, T.1
Yoshimoto, A.2
Sato, S.3
Takamatsu, A.4
-
92
-
-
3843074167
-
The Escherichia coli GTPase CgtAE cofractionates with the 50S ribosomal subunit and interacts with SpoT, a ppGpp synthetase/hydrolase
-
Wout P, Pu K, Sullivan SM, Reese V, Zhou S, et al. (2004) The Escherichia coli GTPase CgtAE cofractionates with the 50S ribosomal subunit and interacts with SpoT, a ppGpp synthetase/hydrolase. J Bacteriol 186: 5249-5257.
-
(2004)
J Bacteriol
, vol.186
, pp. 5249-5257
-
-
Wout, P.1
Pu, K.2
Sullivan, S.M.3
Reese, V.4
Zhou, S.5
-
93
-
-
0017040661
-
Free 3′-OH group of the terminal adenosine of the tRNA molecule is essential for the synthesis in vitro of guanosine tetraphosphate and pentaphosphate in a ribosomal system from Escherichia coli
-
Sprinzl M, Richter D, (1976) Free 3′-OH group of the terminal adenosine of the tRNA molecule is essential for the synthesis in vitro of guanosine tetraphosphate and pentaphosphate in a ribosomal system from Escherichia coli. Eur J Biochem 71: 171-176.
-
(1976)
Eur J Biochem
, vol.71
, pp. 171-176
-
-
Sprinzl, M.1
Richter, D.2
-
94
-
-
58649091749
-
Bacteria possessing two RelA/SpoT-like proteins have evolved a specific stringent response involving the acyl carrier protein-SpoT interaction
-
Battesti A, Bouveret E, (2009) Bacteria possessing two RelA/SpoT-like proteins have evolved a specific stringent response involving the acyl carrier protein-SpoT interaction. J Bacteriol 191: 616-624.
-
(2009)
J Bacteriol
, vol.191
, pp. 616-624
-
-
Battesti, A.1
Bouveret, E.2
-
95
-
-
0035688236
-
Dimerization of the RelA protein of Escherichia coli
-
Yang X, Ishiguro EE, (2001) Dimerization of the RelA protein of Escherichia coli. Biochem Cell Biol 79: 729-736.
-
(2001)
Biochem Cell Biol
, vol.79
, pp. 729-736
-
-
Yang, X.1
Ishiguro, E.E.2
-
96
-
-
78549271503
-
An ancient P-loop GTPase in rice is regulated by a higher plant-specific regulatory protein
-
Cheung MY, Xue Y, Zhou L, Li MW, Sun SS, et al. (2010) An ancient P-loop GTPase in rice is regulated by a higher plant-specific regulatory protein. J Biol Chem.
-
(2010)
J Biol Chem
-
-
Cheung, M.Y.1
Xue, Y.2
Zhou, L.3
Li, M.W.4
Sun, S.S.5
-
97
-
-
79951576033
-
Chlamydia abortus YhbZ, a truncated Obg family GTPase, associates with the Escherichia coli large ribosomal subunit
-
Polkinghorne A, Vaughan L, (2011) Chlamydia abortus YhbZ, a truncated Obg family GTPase, associates with the Escherichia coli large ribosomal subunit. Microb Pathog 50: 200-206.
-
(2011)
Microb Pathog
, vol.50
, pp. 200-206
-
-
Polkinghorne, A.1
Vaughan, L.2
-
98
-
-
79952093554
-
Multispecific recognition: mechanism, evolution, and design
-
Erijman A, Aizner Y, Shifman JM, (2011) Multispecific recognition: mechanism, evolution, and design. Biochemistry 50: 602-611.
-
(2011)
Biochemistry
, vol.50
, pp. 602-611
-
-
Erijman, A.1
Aizner, Y.2
Shifman, J.M.3
-
99
-
-
0017403108
-
Analysis of the relA gene product of Escherichia coli
-
Pedersen F, Kjeldgaard N, (1977) Analysis of the relA gene product of Escherichia coli. Eur J Biochem 76: 91-97.
-
(1977)
Eur J Biochem
, vol.76
, pp. 91-97
-
-
Pedersen, F.1
Kjeldgaard, N.2
-
100
-
-
0003515251
-
Evolution by gene duplication
-
New York, Springer
-
Ohno S, (1970) Evolution by gene duplication. New York Springer.
-
(1970)
-
-
Ohno, S.1
-
101
-
-
75549087305
-
The evolution of gene duplications: classifying and distinguishing between models
-
Innan H, Kondrashov F, (2010) The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet 11: 97-108.
-
(2010)
Nat Rev Genet
, vol.11
, pp. 97-108
-
-
Innan, H.1
Kondrashov, F.2
|