scholarly journals Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotes

1999 ◽  
Vol 15 (7) ◽  
pp. 578-581 ◽  
Author(s):  
Y. Osada ◽  
R. Saito ◽  
M. Tomita
Keyword(s):  
16S Rrna ◽  
Translation Initiation ◽  
Base Pairing

scholarly journals Noncanonical Translation Initiation Comes of Age

2017 ◽  
Vol 199 (14) ◽  
Author(s):  
Paul Babitzke ◽  
Michael O'Connor
Keyword(s):  
16S Rrna ◽  
Translation Initiation ◽  
Regulatory Mechanisms ◽  
Base Pairing ◽  
Initiation Mechanism ◽  
Link Type ◽  
Translation Initiation Mechanism

ABSTRACT The canonical translation initiation mechanism involves base pairing between the mRNA and 16S rRNA. However, a variety of identified mechanisms deviate from this conventional route. Beck and Janssen (J Bacteriol 199:e00091-17, 2017, https://doi.org/10.1128/JB.00091-17 ) have recently described another noncanonical mode of translation initiation. Here, we describe how this process differs from previously reported mechanisms, with the hope that it will foster increased awareness of the diversity of regulatory mechanisms that await discovery.

An mRNA-rRNA base-pairing mechanism for translation initiation in eukaryotes

2005 ◽  
Vol 13 (1) ◽  
pp. 30-34 ◽  
Author(s):  
John Dresios ◽  
Stephen A Chappell ◽  
Wei Zhou ◽  
Vincent P Mauro
Keyword(s):  
Translation Initiation ◽  
Base Pairing ◽  
Pairing Mechanism

scholarly journals The Triticum Mosaic Virus Internal Ribosome Entry Site Relies on a Picornavirus-Like YX-AUG Motif To Designate the Preferred Translation Initiation Site and To Likely Target the 18S rRNA

2018 ◽  
Vol 93 (5) ◽  
Author(s):  
Helena Jaramillo-Mesa ◽  
Megan Gannon ◽  
Elijah Holshbach ◽  
Jincan Zhang ◽  
Robyn Roberts ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Translation Initiation ◽  
Internal Ribosome Entry Site ◽  
18S Rrna ◽  
Initiation Site ◽  
Upstream Region ◽  
Base Pairing ◽  
Entry Site ◽  
Internal Ribosome Entry ◽  
First Report

ABSTRACTSeveral viruses encode an internal ribosome entry site (IRES) at the 5′ end of their RNA, which, unlike most cellular mRNAs, initiates translation in the absence of a 5′ m7GpppG cap. Here, we report a uniquely regulated translation enhancer found in the 739-nucelotide (nt) sequence of the Triticum mosaic virus (TriMV) leader sequence that distinguishes the preferred initiation site from a plethora of IRES-encoded AUG triplets. Through deletion mutations of the TriMV 5′ untranslated region (UTR), we show that the TriMV 5′ UTR encodes acis-acting picornaviral Y16-X11-AUG-like motif with a 16-nt polypyrimidine CU-tract (Y16), at a precise, 11-nt distance (X11) from the preferred 13th AUG. Phylogenetic analyses indicate that this motif is conserved among potyviral leader sequences with multiple AUGs. Consistent with a broadly conserved mechanism, the motif could be functionally replaced with known picornavirus YX-AUG motifs and is predicted to function as target sites for the 18S rRNA by direct base pairing. Accordingly, mutations that disrupted overall complementarity to the 18S rRNA markedly reduced TriMV IRES activity, as did the delivery of antisense oligonucleotides designed to block YX-AUG accessibility. To our knowledge, this is the first report of a plant viral IRES YX-AUG motif, and our findings suggest that a conserved mechanism regulates translation for multiple economically important plant and animal positive single-stranded RNA viruses.IMPORTANCEUncapped viral RNAs often rely on their 5′ leader sequences to initiate translation, and the Triticum mosaic virus (TriMV) devotes an astonishing 7% of its genome to directing ribosomes to the correct AUG. Here we uncover a novel mechanism by which a TriMVcis-regulatory element controls cap-independent translation. The upstream region of the functional AUG contains a 16-nt polypyrimidine tract located 11 nt from the initiation site. Based on functional redundancy with similar motifs derived from human picornaviruses, the motif is likely to operate by directing ribosome targeting through base pairing with 18S rRNA. Our results provide the first report of a broad-spectrum mechanism regulating translation initiation for both plant- and animal-hosted picornaviruses.

scholarly journals Impact of methylations of m2G966/m5C967 in 16S rRNA on bacterial fitness and translation initiation

2012 ◽  
Vol 40 (16) ◽  
pp. 7885-7895 ◽  
Author(s):  
Dmitry E. Burakovsky ◽  
Irina V. Prokhorova ◽  
Petr V. Sergiev ◽  
Pohl Milón ◽  
Olga V. Sergeeva ◽  
...  
Keyword(s):  
16S Rrna ◽  
Translation Initiation ◽  
Bacterial Fitness

scholarly journals Characterization of 16S rRNA mutations that decrease the fidelity of translation initiation

RNA ◽  
2007 ◽  
Vol 13 (12) ◽  
pp. 2348-2355 ◽  
Author(s):  
D. Qin ◽  
N. M. Abdi ◽  
K. Fredrick
Keyword(s):  
16S Rrna ◽  
Translation Initiation

scholarly journals A combination of mRNA features influence the efficiency of leaderless mRNA translation initiation

2021 ◽  
Vol 3 (3) ◽  
Author(s):  
Mohammed-Husain M Bharmal ◽  
Alisa Gega ◽  
Jared M Schrader
Keyword(s):  
16S Rrna ◽  
Translation Initiation ◽  
Untranslated Region ◽  
Mrna Translation ◽  
Start Codon ◽  
Leaderless Mrna ◽  
Shine Dalgarno Sequence ◽  
Relationship Of ◽  
Bacterial Translation

Abstract Bacterial translation is thought to initiate by base pairing of the 16S rRNA and the Shine–Dalgarno sequence in the mRNA’s 5′ untranslated region (UTR). However, transcriptomics has revealed that leaderless mRNAs, which completely lack any 5′ UTR, are broadly distributed across bacteria and can initiate translation in the absence of the Shine–Dalgarno sequence. To investigate the mechanism of leaderless mRNA translation initiation, synthetic in vivo translation reporters were designed that systematically tested the effects of start codon accessibility, leader length, and start codon identity on leaderless mRNA translation initiation. Using these data, a simple computational model was built based on the combinatorial relationship of these mRNA features that can accurately classify leaderless mRNAs and predict the translation initiation efficiency of leaderless mRNAs. Thus, start codon accessibility, leader length, and start codon identity combine to define leaderless mRNA translation initiation in bacteria.

scholarly journals Evidence against an Interaction between the mRNA Downstream Box and 16S rRNA in Translation Initiation

2001 ◽  
Vol 183 (11) ◽  
pp. 3499-3505 ◽  
Author(s):  
Isabella Moll ◽  
Michael Huber ◽  
Sonja Grill ◽  
Pooneh Sairafi ◽  
Florian Mueller ◽  
...  
Keyword(s):  
16S Rrna ◽  
Translation Initiation ◽  
Base Pair ◽  
Translational Efficiency ◽  
Coding Region ◽  
Reporter Construct ◽  
Leaderless Mrna ◽  
30S Subunit ◽  
Downstream Box ◽  
Ribosomal P

ABSTRACT Based on the complementarity of the initial coding region (downstream box [db]) of several bacterial and phage mRNAs to bases 1469 to 1483 in helix 44 of 16S rRNA (anti-downstream box [adb]), it has been proposed that db-adb base pairing enhances translation in a way that is similar to that of the Shine-Dalgarno (SD)/anti-Shine-Dalgarno (aSD) interaction. Computer modeling of helix 44 on the 30S subunit shows that the topography of the 30S ribosome does not allow a simultaneous db-adb interaction and placement of the initiation codon in the ribosomal P site. Thus, the db-adb interaction cannot substitute for the SD-aSD interaction in translation initiation. We have always argued that any contribution of the db-adb interaction should be most apparent on mRNAs devoid of an SD sequence. Here, we show that 30S ribosomes do not bind to leaderless mRNA in the absence of initiator tRNA, even when the initial coding region shows a 15-nucleotide complementarity (optimal fit) with the putative adb. In addition, an optimized db did not affect the translational efficiency of a leaderless λ cI-lacZ reporter construct. Thus, the db-adb interaction can hardly serve as an initial recruitment signal for ribosomes. Moreover, we show that different leaderless mRNAs are translated in heterologous systems although the sequence of the putative adb's within helix 44 of the 30S subunits of the corresponding bacteria differ largely. Taken our data together with those of others (M. O'Connor, T. Asai, C. L. Squires, and A. E. Dahlberg, Proc. Natl. Acad. Sci. USA 96:8973–8978, 1999; A. La Teana, A. Brandi, M. O'Connor, S. Freddi, and C. L. Pon, RNA 6:1393–1402, 2000), we conclude that the db does not base pair with the adb.

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