Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 1999 Jan;181(2):359-67.
doi: 10.1128/JB.181.2.359-367.1999.

Processive antitermination

R A Weisberg  1 , M E Gottesman
Affiliations
Review

Processive antitermination

R A Weisberg et al. J Bacteriol. 1999 Jan.
No abstract available

PubMed Disclaimer

Figures

FIG. 1
FIG. 1
(A) Alignment of phage N proteins and the HK022 Nun protein. The color groupings reflect the frequency of amino acid substitutions in evolutionarily related protein domains: an amino acid is more likely to be replaced by one in the same color group than by one in a different color group in related proteins (34). The amino-proximal ARM regions were aligned by eye and according to the structures of the P22 and λ ARMs complexed to their cognate nut sites (see text and Fig. 2), and the remainder of the proteins was aligned by ClustalW (38). The dots indicate gaps introduced to improve the alignment. Aside from the ARM regions, the proteins fall into three very distantly related (or unrelated) families: (i) λ and phage 21; (ii) P22, phage L, and HK97; and (iii) HK022 Nun. The divergence of Nun from the N proteins is unsurprising because of their different functions. The sequence database was searched for additional N homologs with the PSI-BLAST program (3), using each of the listed sequences as a query, but none were found. Two N proteins were omitted from the alignment: that of phage H19b, because it differs by only three conservative substitutions from N of HK97 (E60D, K80E, and R100K) (3), and that of lambdoid phage φ80 (Phi 80), because it shows no resemblance to any of the other N proteins, lacking even an ARM (42, 69). (B) Alignment of phage Q proteins. The alignments were generated by ClustalW, and the database was searched for Q homologs as described above. These proteins fall into three very distantly related (or unrelated) families: (i) λ and Qin; (ii) H19b, Dlp12, and phage 21; and (iii) N15 and phage 82. Qin and Dlp12 are defective lambdoid prophages of E. coli, but it is likely that their Q proteins are active (see reference 16). The Q proteins of phages HK022 and P22 were omitted from the alignment because of their close similarity to that of λ. A putative and possibly defective Q, encoded by a sequence located upstream of Shiga-like toxin I genes in an E. coli isolate (72) and found by a BLAST search of the translated nucleotide sequence database, was omitted from the alignment because of its close similarity to the Q of phage H19B (61).
FIG. 2
FIG. 2
BOXA and BOXB RNAs and their interaction with the ARM of their cognate N proteins. The amino acid-nucleotide interactions are shown to the left except for BOXB of phage 21, for which the structure of the complex is unknown. The sequences of BOXA and BOXA-BOXB spacer are shown to the right. The dots to the left and right of the spacer sequences are for alignment. (A) λ N-ARM-BOXB complex (adapted from reference with permission of the publisher). Open circles, pentagons, and rectangles represent phosphates, riboses, and bases, respectively. Watson-Crick base pairs (||||) are indicated. The zigzag line denotes a sheared G · A base pair. Open circles, open rectangles, and arrowheads depict ionic, hydrophobic, and hydrogen-bonding interactions, respectively. Guanine-11, indicated by a bold rectangle, is extruded from the BOXB loop (see text). (B) P22 N-ARM-BOXB complex (adapted from reference with permission of the publisher). Open circles, pentagons, rectangles, and ovals represent phosphates, riboses, bases, and amino acids, respectively. The solid pentagons indicate riboses with a C2′-endo pucker. Base stacking (formula image), intermolecular hydrogen bonding or electrostatic interactions (<-----), intermolecular hydrophobic or van der Waals interactions (←), intramolecular hydrogen bonds (––––) and Watson-Crick base pairs (|||||) are indicated. Cytosine-11 is extruded from the loop (see text). Note that the amino-terminal amino acid residue in the complex corresponds to Asn-14 in the complete protein (Fig. 1), and the displayed amino acids are numbered accordingly. (C) NUTL site of phage 21. The arrows indicate the inverted sequence repeats of BOXB.
FIG. 3
FIG. 3
HK022 put sites and folded PUT RNAs. (A) Alignment of putL and putR (43). The numbers give distances from the start sites of the PL and PR promoters, respectively, and the pairs of arrows indicate inverted sequence repeats. (B) Folded PUTL and PUTR RNAs. The structures, which were generated by energy minimization as described (43), have been partially confirmed by genetic and biochemical studies (7, 43).
See this image and copyright information in PMC

References

    1. Aksoy S, Squires C L, Squires C. Evidence for antitermination in Escherichia coli rRNA transcription. J Bacteriol. 1984;159:260–264. - PMC - PubMed
    1. Albrechtsen B, Squires C L, Li S, Squires C. Antitermination of characterized transcriptional terminators by the Escherichia coli rrnG leader region. J Mol Biol. 1990;213:123–134. - PubMed
    1. Altschul S F, Madden T L, Schaffer A A, Zhang J, Zhang Z, Miller W, Lipman D J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402. - PMC - PubMed
    1. Atkinson B L, Gottesman M E. The Escherichia coli rpoB60 mutation blocks antitermination by coliphage HK022 Q-function. J Mol Biol. 1992;227:29–37. - PubMed
    1. Bailey M J, Hughes C, Koronakis V. Increased distal gene transcription by the elongation factor RfaH, a specialized homologue of NusG. Mol Microbiol. 1996;22:729–737. - PubMed

MeSH terms

LinkOut - more resources