The Shine-Dalgarno (SD) sequence is a key element directing the translation to initiate at the authentic start codons and also enabling translation initiation to proceed in 5′ untranslated mRNA regions (5′-UTRs) containing moderately strong secondary structures. Bioinformatic analysis of almost forty genomes from the major bacterial phylum Bacteroidetes revealed, however, a general absence of SD sequence, drop in GC content and consequently reduced tendency to form secondary structures in 5′-UTRs. The experiments using the Prevotella bryantii TC1-1 expression system were in agreement with these findings: neither addition nor omission of SD sequence in the unstructured 5′-UTR affected the level of the reporter protein, non-specific nuclease NucB. Further, NucB level in P. bryantii TC1-1, contrary to hMGFP level in Escherichia coli, was five times lower when SD sequence formed part of the secondary structure with a folding energy -5,2 kcal/mol. Also, the extended SD sequences did not affect protein levels as in E. coli. It seems therefore that a functional SD interaction does not take place during the translation initiation in P. bryanttii TC1-1 and possibly other members of phylum Bacteroidetes although the anti SD sequence is present in 16S rRNA genes of their genomes. We thus propose that in the absence of the SD sequence interaction, the selection of genuine start codons in Bacteroidetes is accomplished by binding of ribosomal protein S1 to unstructured 5′-UTR as opposed to coding region which is inaccessible due to mRNA secondary structure. Additionally, we found that sequence logos of region preceding the start codons may be used as taxonomical markers. Depending on whether complete sequence logo or only part of it, such as information content and base proportion at specific positions, is used, bacterial genera or families and in some cases even bacterial phyla can be distinguished.
References
[1]
Kozak M (2005) Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene 361: 13–37.
[2]
Laursen BS, S？rensen HP, Mortensen KK, Sperling-Petersen HU (2005) Initiation of protein synthesis in bacteria. Microbiol Mol Biol Rev 69: 101–123.
[3]
de Smit MH, van Duin J (1994) Control of translation by mRNA secondary structure in Escherichia coli. J Mol Biol 244: 144–150.
Komarova AV, Tchufistova LS, Supina EV, Boni IV (2002) Protein S1 counteracts the inhibitory effect of the extended Shine-Dalgarno sequence on translation. RNA 8: 1137–1147.
[6]
Vimberg V, Tats A, Remm M, Tenson T (2007) Translation initiation region preferences in Escherichia coli. BMC Mol Biol 8: 100.
[7]
Fargo DC, Zhang M, Gillham NW, Boynton JE (1998) Shine-Dalgarno-like sequences are not required for translation of chloroplast mRNAs in Chlamydomonas reinhardtii chloroplasts or in Escherichia coli. Mol Gen Genet 257: 271–282.
[8]
Moll I, Grill S, Gualerzi CO, Bl？si U (2002) Leaderless mRNA in bacteria: surprises in ribosomal recruitment and translational control. Mol Microbiol 43: 239–246.
[9]
Chang B, Halgamuge S, Tang SL (2006) Analysis of SD sequences in completed microbial genomes: Non-SD-led genes are as common as SD-led genes. Gene 373: 90–99.
[10]
Nakagawa S, Niimura Y, Miura K-I, Gojobori T (2010) Dynamic evolution of translation initiation mechanisms in prokaryotes. Proc Natl Acad Sci U S A 107: 6382–6387.
[11]
Salah P, Bisaglia M, Aliprandi P, Uzan M, Sizun C, et al. (2009) Probing the relationship between Gram-negative and Gram-positive S1 proteins by sequence analysis. Nucleic Acids Res 37: 5578–5588.
[12]
Schneider TD, Stephens RM (1990) Sequence logos: a new way to display consenus sequences. Nucleic Acids Res 18: 6097–6100.
[13]
Miyazaki K, Miyamoto H, Mercer DK, Hirase TMartin, et al. (2003) Involvement of the multidomain regulatory protein XynR in positive control of xylanase gene expression in the ruminal anaerobe Prevotella bryantii B14. J Bacteriol 185: 2219–2226.
[14]
Gupta RS, Lorenzini E (2007) Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species. BMC Evol Biol 7: 71.
[15]
Bayley DP, Rocha ER, Smith CJ (2000) Analysis of cepA and other Bacteroides fragilis genes reveals a unique promoter structure. FEMS Microbiol Lett 193: 149–154.
[16]
Chen S, Bagdasarian M, Kaufman MG, Walker ED (2007) Characterization of strong promoters from an environmental Flavobacterium hibernum strain by using a green fluorescent protein-based reporter system. Appl Environ Microbiol 73: 1089–1100.
[17]
Vingadassalom D, Kolb A, Mayer C, Rybkine T, Collatz F, et al. (2005) An unusual primary sigma factor in the Bacteroidetes phylum. Mol Microbiol 56: 888–902.
[18]
Salyers AA, Bonheyo G, Shoemaker NB (2000) Starting a new genetic system: lessons from Bacteroides. Methods 20: 35–46.
[19]
Accetto T, Avgu？tin G (2007) Studies on Prevotella nuclease using a system for the controlled expression of cloned genes in P. bryantii TC1-1. Microbiol-SGM 153: 2281–2288.
[20]
Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, et al. (2000) Structure of functionally activated small ribosomal subunit at 3.3 ？ resolution. Cell 102: 615–623.
[21]
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406–3415.
[22]
Cerde？o-Tárraga AM, Patrick S, Crossman LC, Blakely G, Abratt V, et al. (2005) Extensive DNA inversions in the B. fragilis genome control variable gene expression. Science 307: 1463–5.
[23]
Kuwahara T, Yamashita A, Hirakawa H, Nakayama H, Toh H, et al. (2004) Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation. Proc Natl Acad Sci U S A 101: 14919–14924.
[24]
Xu J, Bjursell MK, Himrod J, Deng S, Carmichael LK, et al. (2003) A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science 299: 2074–2076.
[25]
Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, et al. (2007) Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol 5: e156.
[26]
Sakamoto M, Benno Y (2006) Reclassification of Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae as Parabacteroides distasonis gen. nov., comb. nov., Parabacteroides goldsteinii comb. nov. and Parabacteroides merdae comb. nov. Int J Syst Evol Microbiol 56: 1599–605.
[27]
Zhu HQ, Hu GQ, Ouyang ZQ, Wang J, She ZS (2004) Accuracy improvement for identifying translation initiation sites in microbial genomes. Bioinformatics 20: 3308–3317.
[28]
Nakamoto T (2007) The initiation of eukaryotic and prokaryotic protein synthesis: A selective accessibility and multisubstrate enzyme reaction. Gene 403: 1–5.
[29]
de Smit MH, van Duin J (1994) Translational initiation on structured messengers. Another role for the Shine-Dalgarno interaction. J Mol Biol 235: 173–184.
[30]
van Gylswyk NO (1990) Enumeration and presumptive identification of some functional groups of bacteria in the rumen of dairy cows fed grass silage-based diets. FEMS Microbiol Ecol 73: 243–254.
[31]
Hobson PN (1969) Rumen bacteria. In: Norris JR, Ribbons DW, editors. Methods in microbiology, Vol 3B. London and New York: Academic press. pp. 133–149.
[32]
Daniel AS, Martin J, Vanat I, Whitehead TR, Flint HJ (1995) Expression of a cloned cellulase/xylanase gene from Prevotella ruminicola in Bacteroides vulgatus, Bacteroides uniformis and Prevotella ruminicola. J Appl Bacteriol 79: 417–424.
[33]
Rice P, Longden I, Bleasby A (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet 16: 276–277.
Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188–1190.
[36]
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947–2948.
[37]
Markham NR, Zuker M (2008) UNAFold: software for nucleic acid folding and hybriziation. In: Keith JM, editor. Bioinformatics, Volume II. Totowa, NJ: Humana Press. pp. 3–31. Structure, Function and Applications, number 453 in Methods in Molecular Biology.
