REFERENCES
1. Caimano, M.J., Drecktrah, D., Kung, F. and Samuels, D.S. (2016)
Interaction of the Lyme disease spirochete with its tick vector.Cell. Microbiol. , 18 , 919-927.
2. Radolf, J.D., Caimano, M.J., Stevenson, B. and Hu, L.T. (2012) Of
ticks, mice and men: understanding the dual-host lifestyle of Lyme
disease spirochaetes. Nat. Rev. Microbiol. , 10 , 87-99.
3. Iyer, R. and Schwartz, I. (2016) Microarray-based comparative genomic
and transcriptome analysis of Borrelia burgdorferi .Microarrays , 5 , 9.
4. Samuels, D.S., Lybecker, M.C., Yang, X.F., Ouyang, Z., Bourret, T.J.,
Boyle, W.K., Stevenson, B., Drecktrah, D. and Caimano, M.J. (2021) Gene
regulation and transcriptomics. Curr. Issues Mol. Biol. ,42 , 223-266.
5. Dunham-Ems, S.M., Caimano, M.J., Pal, U., Wolgemuth, C.W., Eggers,
C.H., Balic, A. and Radolf, J.D. (2009) Live imaging reveals a biphasic
mode of dissemination of Borrelia burgdorferi within ticks.J. Clin. Invest. , 119 , 3652-3665.
6. Ribeiro, J.M.C., Mather, T.N., Piesman, J. and Spielman, A. (1987)
Dissemination and salivary delivery of Lyme disease spirochetes in
vector ticks (Acari: Ixodidae). J. Med. Entomol. , 24 ,
201-205.
7. Fisher, M.A., Grimm, D., Henion, A.K., Elias, A.F., Stewart, P.E.,
Rosa, P.A. and Gherardini, F.C. (2005) Borrelia burgdorferiσ54 is required for mammalian infection and vector
transmission but not for tick colonization. Proc. Natl. Acad. Sci.
USA , 102 , 5162-5167.
8. Caimano, M.J., Iyer, R., Eggers, C.H., Gonzalez, C., Morton, E.A.,
Gilbert, M.A., Schwartz, I. and Radolf, J.D. (2007) Analysis of the RpoS
regulon in Borrelia burgdorferi in response to mammalian host
signals provides insight into RpoS function during the enzootic cycle.Mol. Microbiol. , 65 , 1193-1217.
9. Ouyang, Z., Blevins, J.S. and Norgard, M.V. (2008) Transcriptional
interplay among the regulators Rrp2, RpoN and RpoS in Borrelia
burgdorferi . Microbiology , 154 , 2641-2658.
10. Drecktrah, D., Lybecker, M., Popitsch, N., Rescheneder, P., Hall,
L.S. and Samuels, D.S. (2015) The Borrelia burgdorferi RelA/SpoT
homolog and stringent response regulate survival in the tick vector and
global gene expression during starvation. PLoS Pathog. ,11 , e1005160.
11. Bugrysheva, J.V., Pappas, C.J., Terekhova, D.A., Iyer, R., Godfrey,
H.P., Schwartz, I. and Cabello, F.C. (2015) Characterization of the
RelBbu regulon in Borrelia burgdorferi reveals
modulation of glycerol metabolism by (p)ppGpp. PLoS One ,10 , e0118063.
12. Caimano, M.J., Kenedy, M.R., Kairu, T., Desrosiers, D.C., Harman,
M., Dunham-Ems, S., Akins, D.R., Pal, U. and Radolf, J.D. (2011) The
hybrid histidine kinase Hk1 is part of a two-component system that is
essential for survival of Borrelia burgdorferi in feedingIxodes scapularis ticks. Infect. Immun. , 79 ,
3117-3130.
13. Caimano, M.J., Dunham-Ems, S., Allard, A.M., Cassera, M.B., Kenedy,
M. and Radolf, J.D. (2015) Cyclic di-GMP modulates gene expression in
Lyme disease spirochetes at the tick-mammal interface to promote
spirochete survival during the blood meal and tick-to-mammal
transmission. Infect. Immun. , 83 , 3043-3060.
14. Groshong, A.M., Grassmann, A.A., Luthra, A., McLain, M.A., Provatas,
A.A., Radolf, J.D. and Caimano, M.J. (2021) PlzA is a bifunctional
c-di-GMP biosensor that promotes tick and mammalian host-adaptation ofBorrelia burgdorferi . PLoS Pathog. , 17 , e1009725.
15. Rogers, E.A., Terekhova, D., Zhang, H.-M., Hovis, K.M., Schwartz, I.
and Marconi, R.T. (2009) Rrp1, a cyclic-di-GMP-producing response
regulator, is an important regulator of Borrelia burgdorferi core
cellular functions. Mol. Microbiol. , 71 , 1551-1573.
16. Woodson, S.A., Panja, S. and Santiago-Frangos, A. (2018) Proteins
that chaperone RNA regulation. Microbiol. Spectr. , 6 ,
RWR-0026-2018.
17. Rajkowitsch, L., Chen, D., Stampfl, S., Semrad, K., Waldsich, C.,
Mayer, O., Jantsch, M.F., Konrat, R., Bläsi, U. and Schroeder, R. (2007)
RNA chaperones, RNA annealers and RNA helicases. RNA Biol. ,4 , 118-130.
18. Doetsch, M., Schroeder, R. and Fürtig, B. (2011) Transient
RNA-protein interactions in RNA folding. FEBS J. , 278 ,
1634-1642.
19. Katsuya-Gaviria, K., Paris, G., Dendooven, T. and Bandyra, K.J.
(2022) Bacterial RNA chaperones and chaperone-like riboregulators:
behind the scenes of RNA-mediated regulation of cellular metabolism.RNA Biol. , 19 , 419-436.
20. Djapgne, L. and Oglesby, A.G. (2021) Impacts of small RNAs and their
chaperones on bacterial pathogenicity. Front. Cell. Infect.
Microbiol. , 11 , 604511.
21. Panja, S. and Woodson, S.A. (2012) Hfq proximity and orientation
controls RNA annealing. Nucleic Acids Res. , 40 ,
8690-8697.
22. Olejniczak, M. and Storz, G. (2017) ProQ/FinO-domain proteins:
another ubiquitous family of RNA matchmakers? Mol. Microbiol. ,104 , 905-915.
23. Holmqvist, E., Berggren, S. and Rizvanovic, A. (2020) RNA-binding
activity and regulatory functions of the emerging sRNA-binding protein
ProQ. Biochim. Biophys. Acta Gene Regul. Mech. , 1863 ,
194596.
24. Melamed, S., Adams, P.P., Zhang, A., Zhang, H. and Storz, G. (2020)
RNA-RNA Interactomes of ProQ and Hfq reveal overlapping and competing
roles. Mol. Cell , 77 , 411-425 e417.
25. Lybecker, M.C., Abel, C.A., Feig, A.L. and Samuels, D.S. (2010)
Identification and function of the RNA chaperone Hfq in the Lyme disease
spirochete Borrelia burgdorferi . Mol. Microbiol. ,78 , 622-635.
26. Majdalani, N., Vanderpool, C.K. and Gottesman, S. (2005) Bacterial
small RNA regulators. Crit. Rev. Biochem. Mol. Biol. ,40 , 93-113.
27. Storz, G., Vogel, J. and Wassarman, K.M. (2011) Regulation by small
RNAs in bacteria: expanding frontiers. Mol. Cell , 43 ,
880-891.
28. Caldelari, I., Chao, Y., Romby, P. and Vogel, J. (2013) RNA-mediated
regulation in pathogenic bacteria. Cold Spring Harb. Perspect.
Med. , 3 , a010298.
29. Chakravarty, S. and Massé, E. (2019) RNA-dependent regulation of
virulence in pathogenic bacteria. Front. Cell. Infect.
Microbiol. , 9 , 337.
30. Svensson, S.L. and Sharma, C.M. (2016) Small RNAs in bacterial
virulence and communication. Microbiol. Spectr. , 4 ,
VMBF-0028-2015.
31. Lybecker, M.C. and Samuels, D.S. (2007) Temperature-induced
regulation of RpoS by a small RNA in Borrelia burgdorferi .Mol. Microbiol. , 64 , 1075-1089.
32. Drecktrah, D., Hall, L.S., Brinkworth, A.J., Comstock, J.R.,
Wassarman, K.M. and Samuels, D.S. (2020) Characterization of 6S RNA in
the Lyme disease spirochete. Mol. Microbiol. , 113 ,
399-417.
33. Medina-Pérez, D.N., Wager, B., Troy, E., Gao, L., Norris, S.J., Lin,
T., Hu, L., Hyde, J.A., Lybecker, M. and Skare, J.T. (2020) The
intergenic small non-coding RNA ittA is required for optimal
infectivity and tissue tropism in Borrelia burgdorferi .PLoS Pathog. , 16 , e1008423.
34. Adams, P.P., Flores Avile, C., Popitsch, N., Bilusic, I., Schroeder,
R., Lybecker, M. and Jewett, M.W. (2017) In vivo expression
technology and 5′ end mapping of the Borrelia burgdorferitranscriptome identify novel RNAs expressed during mammalian infection.Nucleic Acids Res. , 45 , 775-792.
35. Lybecker, M.C. and Samuels, D.S. (2017) Small RNAs of Borrelia
burgdorferi : characterizing functional regulators in a sea of sRNAs.Yale J. Biol. Med. , 90 , 317-323.
36. Drecktrah, D., Hall, L.S., Rescheneder, P., Lybecker, M. and
Samuels, D.S. (2018) The stringent response-regulated sRNA transcriptome
of Borrelia burgdorferi . Front. Cell. Infect. Microbiol. ,8 , 231.
37. Popitsch, N., Bilusic, I., Rescheneder, P., Schroeder, R. and
Lybecker, M. (2017) Temperature-dependent sRNA transcriptome of the Lyme
disease spirochete. BMC Genomics , 18 , 28.
38. Arnold, W.K., Savage, C.R., Brissette, C.A., Seshu, J., Livny, J.
and Stevenson, B. (2016) RNA-seq of Borrelia burgdorferi in
multiple phases of growth reveals insights into the dynamics of gene
expression, transcriptome architecture, and noncoding RNAs. PLoS
One , 11 , e0164165.
39. Cotter, P.A. and Stibitz, S. (2007) c-di-GMP-mediated regulation of
virulence and biofilm formation. Curr. Opin. Microbiol. ,10 , 17-23.
40. Wolfe, A.J. and Visick, K.L. (2008) Get the message out:
cyclic-di-GMP regulates multiple levels of flagellum-based motility.J. Bacteriol. , 190 , 463-475.
41. Hengge, R. (2009) Principles of c-di-GMP signalling in bacteria.Nat. Rev. Microbiol. , 7 , 263-273.
42. Römling, U., Galperin, M.Y. and Gomelsky, M. (2013) Cyclic di-GMP:
the first 25 years of a universal bacterial second messenger.Microbiol. Mol. Biol. Rev. , 77 , 1-52.
43. Valentini, M. and Filloux, A. (2019) Multiple roles of c-di-GMP
sgnaling in bacterial pathogenesis. Annu. Rev. Microbiol. ,73 , 387-406.
44. Galperin, M.Y., Nikolskaya, A.N. and Koonin, E.V. (2001) Novel
domains of the prokaryotic two-component signal transduction systems.FEMS Microbiol. Lett. , 203 , 11-21.
45. Sultan, S.Z., Pitzer, J.E., Boquoi, T., Hobbs, G., Miller, M.R. and
Motaleb, M.A. (2011) Analysis of the HD-GYP domain cyclic-di-GMP
phosphodiesterase reveals a role in motility and enzootic life cycle ofBorrelia burgdorferi . Infect. Immun. , 79 ,
3273-3283.
46. Sultan, S.Z., Pitzer, J.E., Miller, M.R. and Motaleb, M.A. (2010)
Analysis of a Borrelia burgdorferi phosphodiesterase demonstrates
a role for cyclic-di-guanosine monophosphate in motility and virulence.Mol. Microbiol. , 77 , 128-142.
47. Novak, E.A., Sultan, S.Z. and Motaleb, M.A. (2014) The cyclic-di-GMP
signaling pathway in the Lyme disease spirochete, Borrelia
burgdorferi . Front. Cell. Infect. Microbiol. , 4 , 56.
48. Bauer, W.J., Luthra, A., Zhu, G., Radolf, J.D., Malkowski, M.G. and
Caimano, M.J. (2015) Structural characterization and modeling of theBorrelia burgdorferi hybrid histidine kinase Hk1 periplasmic
sensor: a system for sensing small molecules associated with tick
feeding. J. Struct. Biol. , 192 , 48-58.
49. He, M., Ouyang, Z., Troxell, B., Xu, H., Moh, A., Piesman, J.,
Norgard, M.V., Gomelsky, M. and Yang, X.F. (2011) Cyclic di-GMP is
essential for the survival of the Lyme disease spirochete in ticks.PLoS Pathog. , 7 , e1002133.
50. Kostick, J.L., Szkotnicki, L.T., Rogers, E.A., Bocci, P., Raffaelli,
N. and Marconi, R.T. (2011) The diguanylate cyclase, Rrp1, regulates
critical steps in the enzootic cycle of the Lyme disease spirochetes.Mol. Microbiol. , 81 , 219-231.
51. Jenal, U., Reinders, A. and Lori, C. (2017) Cyclic di-GMP: second
messenger extraordinaire. Nat. Rev. Microbiol. , 15 ,
271-284.
52. He, M., Zhang, J.-J., Ye, M., Lou, Y. and Yang, X.F. (2014) Cyclic
di-GMP receptor PlzA controls virulence gene expression through RpoS inBorrelia burgdorferi . Infect. Immun. , 82 ,
445-452.
53. Mallory, K.L., Miller, D.P., Oliver, L.D., Jr., Freedman, J.C.,
Kostick-Dunn, J.L., Carlyon, J.A., Marion, J.D., Bell, J.K. and Marconi,
R.T. (2016) Cyclic-di-GMP binding induces structural rearrangements in
the PlzA and PlzC proteins of the Lyme disease and relapsing fever
spirochetes: a possible switch mechanism for c-di-GMP-mediated effector
functions. Pathog. Dis. , 74 , ftw105.
54. Freedman, J.C., Rogers, E.A., Kostick, J.L., Zhang, H., Iyer, R.,
Schwartz, I. and Marconi, R.T. (2010) Identification and molecular
characterization of a cyclic-di-GMP effector protein, PlzA (BB0733):
additional evidence for the existence of a functional cyclic-di-GMP
regulatory network in the Lyme disease spirochete, Borrelia
burgdorferi . FEMS Immunol. Med. Microbiol. , 58 ,
285-294.
55. Pitzer, J.E., Sultan, S.Z., Hayakawa, Y., Hobbs, G., Miller, M.R.
and Motaleb, M.A. (2011) Analysis of the Borrelia burgdorfericyclic-di-GMP-binding protein PlzA reveals a role in motility and
virulence. Infect. Immun. , 79 , 1815-1825.
56. Kostick-Dunn, J.L., Izac, J.R., Freedman, J.C., Szkotnicki, L.T.,
Oliver, L.D., Jr. and Marconi, R.T. (2018) The Borrelia
burgdorferi c-di-GMP binding receptors, PlzA and PlzB, are functionally
distinct. Front. Cell. Infect. Microbiol. , 8 , 213.
57. Zhang, J.-J., Chen, T., Yang, Y., Du, J., Li, H., Troxell, B., He,
M., Carrasco, S.E., Gomelsky, M. and Yang, X.F. (2018) Positive and
negative regulation of glycerol utilization by the c-di-GMP binding
protein PlzA in Borrelia burgdorferi . J. Bacteriol. ,200 , e00243-18.
58. Singh, A., Izac, J.R., Schuler, E.J.A., Patel, D.T., Davies, C. and
Marconi, R.T. (2021) High-resolution crystal structure of theBorreliella burgdorferi PlzA protein in complex with c-di-GMP:
new insights into the interaction of c-di-GMP with the novel xPilZ
domain. Pathog. Dis. , 79 .
59. Samuels, D.S., Drecktrah, D. and Hall, L.S. (2018) In Pal, U. and
Buyuktanir, O. (eds.), Borrelia burgdorferi: Methods and
Protocols . Humana Press, New York, NY, Vol. 1690, pp. 183-200.
60. Brandt, K.S., Horiuchi, K., Biggerstaff, B.J. and Gilmore, R.D.
(2019) Evaluation of patient IgM and IgG reactivity against multiple
antigens for improvement of serodiagnostic testing for early Lyme
disease. Front. in Public Health , 7 , 370.
61. Samuels, D.S., Mach, K.E. and Garon, C.F. (1994) Genetic
transformation of the Lyme disease agent Borrelia burgdorferiwith coumarin-resistant gyrB . J. Bacteriol. , 176 ,
6045-6049.
62. Pace, C.N., Vajdos, F., Fee, L., Grimsley, G. and Gray, T. (1995)
How to measure and predict the molar absorption coefficient of a
protein. Protein Sci. , 4 , 2411-2423.
63. Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S.e., Wilkins,
M.R., Appel, R.D. and Bairoch, A. (2005) In Walker, J. M. (ed.),The Proteomics Protocols Handbook . Humana Press, Totowa, NJ, pp.
571-607.
64. Heinig, M. and Frishman, D. (2004) STRIDE: a web server for
secondary structure assignment from known atomic coordinates of
proteins. Nucleic Acids Res. , 32 , W500-W502.
65. Miles, A.J., Ramalli, S.G. and Wallace, B.A. (2022) DichroWeb, a
website for calculating protein secondary structure from circular
dichroism spectroscopic data. Protein Sci. , 31 , 37-46.
66. Lees, J.G., Miles, A.J., Wien, F. and Wallace, B.A. (2006) A
reference database for circular dichroism spectroscopy covering fold and
secondary structure space. Bioinformatics , 22 ,
1955-1962.
67. Sreerama, N. and Woody, R.W. (2000) Estimation of protein secondary
structure from circular dichroism spectra: comparison of CONTIN, SELCON,
and CDSSTR methods with an expanded reference set. Anal.
Biochem. , 287 , 252-260.
68. Doetsch, M., Fürtig, B., Gstrein, T., Stampfl, S. and Schroeder, R.
(2011) The RNA annealing mechanism of the HIV-1 Tat peptide: conversion
of the RNA into an annealing-competent conformation. Nucleic Acids
Res. , 39 , 4405-4418.
69. Rajkowitsch, L., Semrad, K., Mayer, O. and Schroeder, R. (2005)
Assays for the RNA chaperone activity of proteins. Biochem. Soc.
Trans. , 33 , 450-456.
70. Boyle, W.K., Hall, L.S., Armstrong, A.A., Dulebohn, D.P., Samuels,
D.S., Gherardini, F.C. and Bourret, T.J. (2020) Establishment of anin vitro RNA polymerase transcription system: a new tool to study
transcriptional activation in Borrelia burgdorferi . Sci.
Rep. , 10 , 8246.
71. Doetsch, M., Gstrein, T., Schroeder, R. and Fürtig, B. (2010)
Mechanisms of StpA-mediated RNA remodeling. RNA Biol. ,7 , 735-743.
72. Ammerman, M.L., Presnyak, V., Fisk, J.C., Foda, B.M. and Read, L.K.
(2010) TbRGG2 facilitates kinetoplastid RNA editing initiation and
progression past intrinsic pause sites. RNA , 16 ,
2239-2251.
73. Bae, W., Xia, B., Inouye, M. and Severinov, K. (2000)Escherichia coli CspA-family RNA chaperones are transcription
antiterminators. Proc. Natl. Acad. Sci. USA , 97 ,
7784-7789.
74. Landick, R., Stewart, J. and Lee, D.N. (1990) Amino acid changes in
conserved regions of the β-subunit of Escherichia coli RNA
polymerase alter transcription pausing and termination. Genes
Dev. , 4 , 1623-1636.
75. Lybecker, M., Zimmermann, B., Bilusic, I., Tukhtubaeva, N. and
Schroeder, R. (2014) The double-stranded transcriptome ofEscherichia coli . Proc. Natl. Acad. Sci. USA ,111 , 3134-3139.
76. Chaulk, S.G., Smith-Frieday, M.N., Arthur, D.C., Culham, D.E.,
Edwards, R.A., Soo, P., Frost, L.S., Keates, R.A.B., Glover, J.N.M. and
Wood, J.M. (2011) ProQ is an RNA chaperone that controls ProP levels inEscherichia coli . Biochemistry , 50 , 3095-3106.
77. Smirnov, A., Förstner, K.U., Holmqvist, E., Otto, A., Günster, R.,
Becher, D., Reinhardt, R. and Vogel, J. (2016) Grad-seq guides the
discovery of ProQ as a major small RNA-binding protein. Proc.
Natl. Acad. Sci. USA , 113 , 11591-11596.
78. Gonzalez, G.M., Hardwick, S.W., Maslen, S.L., Skehel, J.M.,
Holmqvist, E., Vogel, J., Bateman, A., Luisi, B.F. and Broadhurst, R.W.
(2017) Structure of the Escherichia coli ProQ RNA-binding
protein. RNA , 23 , 696-711.
79. Smirnov, A., Wang, C., Drewry, L.L. and Vogel, J. (2017) Molecular
mechanism of mRNA repression in trans by a ProQ-dependent small
RNA. EMBO J. , 36 , 1029-1045.
80. Doetsch, M., Stampfl, S., Fürtig, B., Beich-Frandsen, M., Saxena,
K., Lybecker, M. and Schroeder, R. (2013) Study of E. coli Hfq’s
RNA annealing acceleration and duplex destabilization activities using
substrates with different GC-contents. Nucleic Acids Res. ,41 , 487-497.
81. Mayer, O., Rajkowitsch, L., Lorenz, C., Konrat, R. and Schroeder, R.
(2007) RNA chaperone activity and RNA-binding properties of the E.
coli protein StpA. Nucleic Acids Res. , 35 , 1257-1269.
82. Rajkowitsch, L. and Schroeder, R. (2007) Coupling RNA annealing and
strand displacement: a FRET-based microplate reader assay for RNA
chaperone activity. Biotechniques , 43 , 304-310.
83. Babitzke, P., Lai, Y.-J., Renda, A.J. and Romeo, T. (2019)
Posttranscription initiation control of gene expression mediated by
bacterial RNA-binding proteins. Annu. Rev. Microbiol. ,73 , 43-67.
84. Li, J., Zhang, B., Zhou, L., Qi, L., Yue, L., Zhang, W., Cheng, H.,
Whitman, W.B. and Dong, X. (2019) The archaeal RNA chaperone TRAM0076
shapes the transcriptome and optimizes the growth of Methanococcus
maripaludis . PLoS Genet. , 15 , e1008328.
85. Phadtare, S., Tyagi, S., Inouye, M. and Severinov, K. (2002) Three
amino acids in Escherichia coli CspE surface-exposed aromatic
patch are critical for nucleic acid melting activity leading to
transcription antitermination and cold acclimation of cells. J.
Biol. Chem. , 277 , 46706-46711.
86. Nakaminami, K., Karlson, D.T. and Imai, R. (2006) Functional
conservation of cold shock domains in bacteria and higher plants.Proc. Natl. Acad. Sci. USA , 103 , 10122-10127.
87. Stampfl, S., Doetsch, M., Beich-Frandsen, M. and Schroeder, R.
(2013) Characterization of the kinetics of RNA annealing and strand
displacement activities of the E. coli DEAD-box helicase CsdA.RNA Biol. , 10 , 149-156.
88. Rajkowitsch, L. and Schroeder, R. (2007) Dissecting RNA chaperone
activity. RNA , 13 , 2053-2060.
89. Povolotsky, T.L. and Hengge, R. (2016) Genome-based comparison of
cyclic di-GMP signaling in pathogenic and commensal Escherichia
coli strains. J. Bacteriol. , 198 , 111-126.
90. Youkharibache, P., Veretnik, S., Li, Q., Stanek, K.A., Mura, C. and
Bourne, P.E. (2019) The small β-Barrel domain: a survey-based structural
analysis. Structure , 27 , 6-26.
91. Phadtare, S. and Severinov, K. (2010) RNA remodeling and gene
regulation by cold shock proteins. RNA Biol. , 7 ,
788-795.
92. Rennella, E., Sára, T., Juen, M., Wunderlich, C., Imbert, L.,
Solyom, Z., Favier, A., Ayala, I., Weinhäupl, K., Schanda, P. et
al. (2017) RNA binding and chaperone activity of the E. colicold-shock protein CspA. Nucleic Acids Res. , 45 ,
4255-4268.
93. Hall, K.B. (2017) RNA and proteins: mutual respect. F1000Res ,6 , 345.
94. Allers, J. and Shamoo, Y. (2001) Structure-based analysis of
protein-RNA interactions using the program ENTANGLE. J. Mol.
Biol. , 311 , 75-86.
95. Bercy, M. and Bockelmann, U. (2015) Hairpins under tension: RNA
versus DNA. Nucleic Acids Res. , 43 , 9928-9936.
96. Corley, M., Burns, M.C. and Yeo, G.W. (2020) How RNA-binding
proteins interact with RNA: molecules and mechanisms. Mol. Cell ,78 , 9-29.
97. Hoffman, M.M., Khrapov, M.A., Cox, J.C., Yao, J., Tong, L. and
Ellington, A.D. (2004) AANT: the amino acid-nucleotide interaction
database. Nucleic Acids Res. , 32 , D174-D181.
98. Jones, S., Daley, D.T.A., Luscombe, N.M., Berman, H.M. and Thornton,
J.M. (2001) Protein-RNA interactions: a structural analysis.Nucleic Acids Res. , 29 , 943-954.
99. Luscombe, N.M., Laskowski, R.A. and Thornton, J.M. (2001) Amino
acid-base interactions: a three-dimensional analysis of protein-DNA
interactions at an atomic level. Nucleic Acids Res. , 29 ,
2860-2874.
100. Hudson, W.H. and Ortlund, E.A. (2014) The structure, function and
evolution of proteins that bind DNA and RNA. Nat. Rev. Mol .Cell.
Biol. , 15 , 749-760.
101. Takada, A., Wachi, M., Kaidow, A., Takamura, M. and Nagai, K.
(1997) DNA binding properties of the hfq gene product ofEscherichia coli . Biochem. Biophys. Res. Commun. ,236 , 576-579.
102. Zhang, A., Rimsky, S., Reaban, M.E., Buc, H. and Belfort, M. (1996)Escherichia coli protein analogs StpA and H-NS: regulatory loops,
similar and disparate effects on nucleic acid dynamics. EMBO J. ,15 , 1340-1349.