References
1. Yutin N, Puigbò P, Koonin E V, Wolf YI. Phylogenomics of prokaryotic ribosomal proteins. Lespinet O, ed. PLoS One . 2012;7(5):e36972. doi:10.1371/journal.pone.0036972
2. Pilla SP, Bahadur RP. Residue conservation elucidates the evolution of r-proteins in ribosomal assembly and function. Int J Biol Macromol . 2019;140:323-329. doi:10.1016/j.ijbiomac.2019.08.127
3. Roberts E, Sethi A, Montoya J, Woese CR, Luthey-Schulten Z. Molecular signatures of ribosomal evolution. Proc Natl Acad Sci U S A . 2008;105(37):13953-13958. doi:10.1073/pnas.0804861105
4. Lecompte O, Ripp R, Thierry J-C, Moras D, Poch O. Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale. Nucleic Acids Res . 2002;30(24):5382-5390. doi:10.1093/nar/gkf693
5. Ramulu HG, Groussin M, Talla E, Planel R, Daubin V, Brochier-Armanet C. Ribosomal proteins: Toward a next generation standard for prokaryotic systematics? Mol Phylogenet Evol . 2014;75(1):103-117. doi:10.1016/j.ympev.2014.02.013
6. Machulin A, Deryusheva E, Lobanov M, Galzitskaya O. Repeats in S1 proteins: flexibility and tendency for intrinsic disorder. Int J Mol Sci . 2019;20(10):2377. doi:10.3390/ijms20102377
7. Deryusheva EI, Machulin A V., Matyunin MA, Galzitskaya O V. Investigation of the relationship between the S1 domain and its molecular functions derived from studies of the tertiary structure.Molecules . 2019;24(20):3681. doi:10.3390/molecules24203681
8. Deryusheva EI, Machulin A V., Selivanova OM, Galzitskaya O V. Taxonomic distribution, repeats, and functions of the S1 domain-containing proteins as members of the OB-fold family.Proteins Struct Funct Bioinforma . 2017;85(4):602-613. doi:10.1002/prot.25237
9. Machulin A V, Deryusheva EI, Selivanova OM, Galzitskaya O V. The number of domains in the ribosomal protein S1 as a hallmark of the phylogenetic grouping of bacteria. PLoS One . 2019;14(8):e0221370. doi:10.1371/journal.pone.0221370
10. Sørensen MA, Fricke J, Pedersen S. Ribosomal protein S1 is required for translation of most, if not all, natural mRNAs in Escherichia coli in vivo. J Mol Biol . 1998;280(4):561-569. doi:10.1006/jmbi.1998.1909
11. Okada T, Wower IK, Wower J, Zwieb CW, Kimura M. Contribution of the second OB fold of ribosomal protein S1 from Escherichia coli to the recognition of tmRNA. Biosci Biotechnol Biochem . 2004;68(11):2319-2325. doi:10.1271/bbb.68.2319
12. Skouv J, Schnier J, Rasmussen MD, Subramanian AR, Pedersen S. Ribosomal protein S1 of Escherichia coli is the effector for the regulation of its own synthesis. J Biol Chem . 1990;265(28):17044-17049. Accessed January 19, 2017. http://www.ncbi.nlm.nih.gov/pubmed/2120211
13. Subramanian AR. Structure and functions of ribosomal protein S1.Prog Nucleic Acid Res Mol Biol . 1983;28:101-142. Accessed November 2, 2012. http://www.ncbi.nlm.nih.gov/pubmed/6348874
14. Boni I V, Artamonova VS, Dreyfus M. The last RNA-binding repeat of the Escherichia coli ribosomal protein S1 is specifically involved in autogenous control. J Bacteriol . 2000;182(20):5872-5879. doi:10.1128/JB.182.20.5872-5879.2000
15. Guerrier-Takada C, Subramanian AR, Cole PE. The activity of discrete fragments of ribosomal protein S1 in Q beta replicase function. J Biol Chem . 1983;258(22):13649-13652. http://www.ncbi.nlm.nih.gov/pubmed/6358207
16. Bisaglia M, Laalami S, Uzan M, Bontems F. Activation of the RegB endoribonuclease by the S1 ribosomal protein is due to cooperation between the S1 four C-terminal modules in a substrate-dependant manner.J Biol Chem . 2003;278(17):15261-15271. doi:10.1074/jbc.M212731200
17. Salah P, Bisaglia M, Aliprandi P, Uzan M, Sizun C, Bontems F. Probing the relationship between gram-negative and gram-positive S1 proteins by sequence analysis. Nucleic Acids Res . 2009;37(16):5578-5588. doi:10.1093/nar/gkp547
18. Deryusheva EI, Selivanova OM, Serdyuk IN. Loops and repeats in proteins as footprints of molecular evolution. Biochemistry (Mosc) . 2012;77(13):1487-1499. doi:10.1134/S000629791213007X
19. Duan H, Liu G, Wang X, et al. Evaluation of the ribosomal protein S1 gene (rpsA) as a novel biomarker for Mycobacterium species identification. Biomed Res Int . 2015;2015:271728. doi:10.1155/2015/271728
20. Cock PJA, Antao T, Chang JT, et al. Biopython: Freely available Python tools for computational molecular biology and bioinformatics.Bioinformatics . 2009;25(11):1422-1423. doi:10.1093/bioinformatics/btp163
21. Mukherjee S, Stamatis D, Bertsch J, et al. Genomes OnLine database (GOLD) v.7: Updates and new features. Nucleic Acids Res . 2019;47(D1):D649-D659. doi:10.1093/nar/gky977
22. Letunic I, Bork P. 20 years of the SMART protein domain annotation resource. Nucleic Acids Res . 2018;46(D1):D493-D496. doi:10.1093/nar/gkx922
23. Bateman A, Martin MJ, O’Donovan C, et al. UniProt: A hub for protein information. Nucleic Acids Res . 2015;43(D1):D204-D212. doi:10.1093/nar/gku989
24. Crooks GE, Hon G, Chandonia J-M, Brenner SE. WebLogo: a sequence logo generator. Genome Res . 2004;14(6):1188-1190. doi:10.1101/gr.849004
25. Goldman N, Yang Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol . 1994;11(5):725-736. doi:10.1093/oxfordjournals.molbev.a040153
26. Ludwig W, Klenk H-P. Overview: A Phylogenetic Backbone and Taxonomic Framework for Procaryotic Systematics. In: Bergey’s Manual® of Systematic Bacteriology . Springer New York; 2001:49-65. doi:10.1007/978-0-387-21609-6_8
27. Gupta RS. The phylogeny and signature sequences characteristics of Fibrobacteres, Chlorobi, and Bacteroidetes. Crit Rev Microbiol . 2004;30(2):123-143. doi:10.1080/10408410490435133
28. Gupta. Molecular signatures for the PVC clade (Planctomycetes, Verrucomicrobia, Chlamydiae, and Lentisphaerae) of bacteria provide insights into their evolutionary relationships. Front Microbiol . 2012;3:327. doi:10.3389/fmicb.2012.00327
29. Battistuzzi FU, Feijao A, Hedges SB. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol Biol . 2004;4:44. doi:10.1186/1471-2148-4-44
30. Sekiguchi Y, Ohashi A, Parks DH, Yamauchi T, Tyson GW, Hugenholtz P. First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking. PeerJ . 2015;3(1):e740. doi:10.7717/peerj.740
31. Yarza P, Yilmaz P, Pruesse E, et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol . 2014;12(9):635-645. doi:10.1038/nrmicro3330
32. Hug LA, Baker BJ, Anantharaman K, et al. A new view of the tree of life. Nat Microbiol . 2016;1(5):16048. doi:10.1038/nmicrobiol.2016.48
33. Nikolaki S, Tsiamis G. Microbial diversity in the era of omic technologies. Biomed Res Int . 2013;2013:958719. doi:10.1155/2013/958719
34. Hugenholtz P. Exploring prokaryotic diversity in the genomic era.Genome Biol . 2002;3(2):REVIEWS0003. doi:10.1186/gb-2002-3-2-reviews0003
35. Bertani I, Abbruscato P, Piffanelli P, Subramoni S, Venturi V. Rice bacterial endophytes: Isolation of a collection, identification of beneficial strains and microbiome analysis. Environ Microbiol Rep . 2016;8(3):388-398. doi:10.1111/1758-2229.12403
36. Kolton M, Sela N, Elad Y, Cytryn E. Comparative genomic analysis indicates that niche adaptation of terrestrial Flavobacteria is strongly linked to plant glycan metabolism. Robinson DA, ed. PLoS One . 2013;8(9):e76704. doi:10.1371/journal.pone.0076704
37. Hartman K, van der Heijden MGA, Roussely-Provent V, Walser J-C, Schlaeppi K. Deciphering composition and function of the root microbiome of a legume plant. Microbiome . 2017;5(1):2. doi:10.1186/s40168-016-0220-z
38. Grishin SY, Deryusheva EI, Machulin A V., et al. Amyloidogenic Propensities of Ribosomal S1 Proteins: Bioinformatics Screening and Experimental Checking. Int J Mol Sci . 2020;21(15):5199. doi:10.3390/ijms21155199
39. Agrawal V, Kishan KVR. OB-fold: growing bigger with functional consistency. Curr Protein Pept Sci . 2003;4(3):195-206. doi:10.2174/1389203033487207
40. Sirand-Pugnet P, Lartigue C, Marenda M, et al. Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome.PLoS Genet . 2007;3(5):744-758. doi:10.1371/journal.pgen.0030075
41. Amblar M, Barbas A, Gomez-Puertas P, Arraiano CM. The role of the S1 domain in exoribonucleolytic activity: substrate specificity and multimerization. RNA . 2007;13(3):317-327. doi:10.1261/rna.220407
42. Jeffares DC, Tomiczek B, Sojo V, dos Reis M. A beginners guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome. Methods Mol Biol . 2015;1201:65-90. doi:10.1007/978-1-4939-1438-8_4
43. Kosiol C, Vinar T, da Fonseca RR, et al. Patterns of positive selection in six Mammalian genomes. Schierup MH, ed. PLoS Genet . 2008;4(8):e1000144. doi:10.1371/journal.pgen.1000144
44. Yang Z, Bielawski JP. Statistical methods for detecting molecular adaptation. Trends Ecol Evol . 2000;15(12):496-503. doi:10.1016/S0169-5347(00)01994-7
45. Swanson WJ, Yang Z, Wolfner MF, Aquadro CF. Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals. Proc Natl Acad Sci U S A . 2001;98(5):2509-2514. doi:10.1073/pnas.051605998
46. Anisimova M, Bielawski JP, Yang Z. Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution.Mol Biol Evol . 2001;18(8):1585-1592. doi:10.1093/oxfordjournals.molbev.a003945
47. Bycroft M, Hubbard TJ, Proctor M, Freund SM, Murzin AG. The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold. Cell . 1997;88(2):235-242. doi:10.1016/S0092-8674(00)81844-9
48. Bhattacharjee N, Biswas P. Position-specific propensities of amino acids in the β-strand. BMC Struct Biol . 2010;10(1):29. doi:10.1186/1472-6807-10-29
49. Richardson JS, Richardson DC. Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation. Proc Natl Acad Sci U S A . 2002;99(5):2754-2759. doi:10.1073/pnas.052706099
50. Andrade MA, Perez-Iratxeta C, Ponting CP. Protein repeats: structures, functions, and evolution. J Struct Biol . 2001;134(2-3):117-131. doi:10.1006/jsbi.2001.4392
51. Ponting CP, Russell RB. Identification of distant homologues of fibroblast growth factors suggests a common ancestor for all beta-trefoil proteins. J Mol Biol . 2000;302(5):1041-1047. doi:10.1006/jmbi.2000.4087
52. Battistuzzi FU, Hedges SB. A major clade of prokaryotes with ancient adaptations to life on land. Mol Biol Evol . 2009;26(2):335-343. doi:10.1093/molbev/msn247
53. Robertson L a., Kuenen JG. The Prokaryotes . Vol Volume 5. (Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E, eds.). Springer New York; 2006. doi:10.1007/0-387-30745-1
54. Williams KP, Kelly DP. Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria. Int J Syst Evol Microbiol . 2013;63(PART8):2901-2906. doi:10.1099/ijs.0.049270-0
55. Gupta RS. The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes. FEMS Microbiol Rev . 2000;24(4):367-402. doi:10.1111/j.1574-6976.2000.tb00547.x
56. Gupta RS, Sneath PHA. Application of the character compatibility approach to generalized molecular sequence data: Branching order of the proteobacterial subdivisions. J Mol Evol . 2007;64(1):90-100. doi:10.1007/s00239-006-0082-2
57. Griffiths E, Gupta RS. Signature sequences in diverse proteins provide evidence for the late divergence of the Order Aquificales.Int Microbiol . 2004;7(1):41-52. doi:10.2436/im.v7i1.9443
58. Boussau B, Guéguen L, Gouy M. Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria. BMC Evol Biol . 2008;8(1):272. doi:10.1186/1471-2148-8-272
59. Kielak AM, Barreto CC, Kowalchuk GA, van Veen JA, Kuramae EE. The Ecology of Acidobacteria: Moving beyond Genes and Genomes. Front Microbiol . 2016;7(MAY):744. doi:10.3389/fmicb.2016.00744
60. Spring S, Schulze R, Overmann J, Schleifer K-H. Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes: molecular and cultivation studies. FEMS Microbiol Rev . 2000;24(5):573-590. doi:10.1111/j.1574-6976.2000.tb00559.x
61. Smit E, Leeflang P, Gommans S, van den Broek J, van Mil S, Wernars K. Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl Environ Microbiol . 2001;67(5):2284-2291. doi:10.1128/AEM.67.5.2284-2291.2001
62. Olson CM, Fikrig E, Anguita J. Host defenses to spirochetes. In:Clinical Immunology: Principles and Practice: Fourth Edition . Elsevier Inc.; 2013:338-345. doi:10.1016/B978-0-7234-3691-1.00016-7
63. Kamneva OK, Knight SJ, Liberles DA, Ward NL. Analysis of genome content evolution in pvc bacterial super-phylum: assessment of candidate genes associated with cellular organization and lifestyle. Genome Biol Evol . 2012;4(12):1375-1390. doi:10.1093/gbe/evs113
64. Cho JC, Vergin KL, Morris RM, Giovannoni SJ. Lentisphaera araneosa gen. nov., sp. nov, a transparent exopolymer producing marine bacterium, and the description of a novel bacterial phylum, Lentisphaerae.Environ Microbiol . 2004;6(6):611-621. doi:10.1111/j.1462-2920.2004.00614.x
65. Mendes R, Garbeva P, Raaijmakers JM. The rhizosphere microbiome: Significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev . 2013;37(5):634-663. doi:10.1111/1574-6976.12028
66. Thomas F, Hehemann J-H, Rebuffet E, Czjzek M, Michel G. Environmental and gut bacteroidetes: the food connection. Front Microbiol . 2011;2(MAY):93. doi:10.3389/fmicb.2011.00093
67. Shih PM, Hemp J, Ward LM, Matzke NJ, Fischer WW. Crown group Oxyphotobacteria postdate the rise of oxygen. Geobiology . 2017;15(1):19-29. doi:10.1111/gbi.12200
68. Xiong J. Molecular Evidence for the Early Evolution of Photosynthesis. Science (80- ) . 2000;289(5485):1724-1730. doi:10.1126/science.289.5485.1724
69. Blankenship RE. Origin and early evolution of photosynthesis.Photosynth Res . 1992;33(2):91-111. doi:10.1007/BF00039173
70. Lang JM, Darling AE, Eisen JA. Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. Planet PJ, ed. PLoS One . 2013;8(4):e62510. doi:10.1371/journal.pone.0062510
71. Rinke C, Schwientek P, Sczyrba A, et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature . 2013;499(7459):431-437. doi:10.1038/nature12352
72. Neimark H. Phylogenetic relationships between mycoplasmas and other prokaryotes. The mycoplasmas . 1979;1:43-61. doi:10.1099/00207713-42-2-226
73. Bhugra B, Dybvig K. High-frequency rearrangements in the chromosome of Mycoplasma pulmonis correlate with phenotypic switching. Mol Microbiol . 1992;6(9):1149-1154. doi:10.1111/j.1365-2958.1992.tb01553.x
74. Borkhsenius SN, Chernova OA, Chernov VM, Vonsky MS.Mycoplasmas [in Russian] . Nauka; 2002.
75. Blanchard A. Ureaplasma urealyticum urease genes; use of a UGA tryptophan codon. Mol Microbiol . 1990;4(4):669-676. doi:10.1111/j.1365-2958.1990.tb00636.x