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EcoSal Plus

Domain 4:

Synthesis and Processing of Macromolecules

Nus Factors of

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  • Authors: Ranjan Sen1, Jisha Chalissery2, and Ghazala Muteeb3
  • Editor: Susan T. Lovett4
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad 500076, India; 2: Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad 500076, India; 3: Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad 500076, India; 4: Brandeis University, Waltham, MA
  • Received 13 September 2007 Accepted 30 November 2007 Published 18 January 2008
  • Address correspondence to Ranjan Sen rsen@cdfd.org.in.
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  • Abstract:

    The Nus factors—NusA, NusB, NusE, and NusG—area set of well-conserved proteins in bacteria and are involved in transcription elongation, termination, antitermination, and translation processes. Originally, host mutations defective for supporting bacteriophage λ N-mediated antitermination were mapped to the (), (), and () genes, and hence, these genes were named for tilization ubstances (Nus). Subsequently,the Nus factors were purified and their roles in different host functions were elucidated. Except for NusB, deletion of which is conditionally lethal, all the other Nus factors are essential for . Among the Nus factors, NusA has the most varied functions. It specifically binds to RNA polymerase (RNAP), nascent RNA, and antiterminator proteins like N and Q and hence takes part in modulating transcription elongation, termination, and antitermination. It is also involved in DNA repair pathways. NusG interacts with RNAP and the transcription termination factor Rho and therefore is involved in both factor-dependent termination and transcription elongation processes. NusB and NusE are mostly important in antitermination at the ribosomal operon-transcription. NusE is a component of ribosome and may take part in facilitating the coupling between transcription and translation. This chapter emphasizes the structure-function relationship of these factors and their involvement in different fundamental cellular processes from a mechanistic angle.

  • Citation: Sen R, Chalissery J, Muteeb G. 2008. Nus Factors of , EcoSal Plus 2008; doi:10.1128/ecosalplus.4.5.3.1

Key Concept Ranking

Transcription Elongation Factors
0.4233955
Transcription Elongation
0.40387386
Ribosome Binding Site
0.39451215
Transcription Termination
0.39322895
Transcription Initiation
0.38882956
Rho-Dependent Termination
0.36919332
0.4233955

Article Version

An updated version has been published for this content:
Nus Factors of

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ecosalplus.4.5.3.1.citations
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/content/journal/ecosalplus/10.1128/ecosalplus.4.5.3.1
2008-01-18
2017-07-27

Abstract:

The Nus factors—NusA, NusB, NusE, and NusG—area set of well-conserved proteins in bacteria and are involved in transcription elongation, termination, antitermination, and translation processes. Originally, host mutations defective for supporting bacteriophage λ N-mediated antitermination were mapped to the (), (), and () genes, and hence, these genes were named for tilization ubstances (Nus). Subsequently,the Nus factors were purified and their roles in different host functions were elucidated. Except for NusB, deletion of which is conditionally lethal, all the other Nus factors are essential for . Among the Nus factors, NusA has the most varied functions. It specifically binds to RNA polymerase (RNAP), nascent RNA, and antiterminator proteins like N and Q and hence takes part in modulating transcription elongation, termination, and antitermination. It is also involved in DNA repair pathways. NusG interacts with RNAP and the transcription termination factor Rho and therefore is involved in both factor-dependent termination and transcription elongation processes. NusB and NusE are mostly important in antitermination at the ribosomal operon-transcription. NusE is a component of ribosome and may take part in facilitating the coupling between transcription and translation. This chapter emphasizes the structure-function relationship of these factors and their involvement in different fundamental cellular processes from a mechanistic angle.

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Figures

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Figure 1

Positions of the respective genes are boxed. The directions of the arrows indicate the directions of transcription. Numbers at both sides indicate the nucleotide sequence positions.

Citation: Sen R, Chalissery J, Muteeb G. 2008. Nus Factors of , EcoSal Plus 2008; doi:10.1128/ecosalplus.4.5.3.1
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Figure 2

(A) Cartoon showing different functional domains of NusA. The NTD and the Src homology (S1), KH1, and KH2 domains are highly conserved among different NusA molecules. Domains AR1 and AR2 are found in a few species, including . Numbers indicate amino acid positions. (B) The crystal structure of conserved domains of NusA from (Protein Data Bank [PDB] no. 1L2F) ( 36 ) shows that each functional domain has distinct tertiary folds and corresponds to a separate structural domain, as indicated. (C) Two separate nuclear magnetic resonance structures of AR1 and AR2 domains (PDB nos. 1WCL and 1WCN, respectively) ( 37 ) of . (D) Crystal structure of NusA (pink) with the stem-loop RNA (black) from of an rRNA operon (corresponding to PDB no. 2ASB) ( 30 ). The structure revealed that both the RNA binding domains KH1 and KH2 take part in the interaction with the RNA and that the interaction destabilizes the stem-loop structure of . (E) Solution structure of the central part of N protein (shown as a green thread) from bacteriophage λ in a complex with the dimeric interface of the AR1 domain of NusA (PDB no. 1U9L) ( 31 ). The dimeric interface was found to be formed from two AR1 domains coming from two NusA molecules. The region encompassing residues 352 to 419 of one NusA molecule (in orange) dimerizes with the region encompassing residues 352 to 421 of the second NusA molecule (blue). This indicates that in the antitermination complex with λ N protein, NusA may form a dimer. Amino acid numbers of the relevant region of the λ N protein are indicated.

Citation: Sen R, Chalissery J, Muteeb G. 2008. Nus Factors of , EcoSal Plus 2008; doi:10.1128/ecosalplus.4.5.3.1
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Image of Figure 3
Figure 3

(A) Solution structure of NusB (PDB no. 1EY1) ( 44 ), consisting of N- and C-terminal globular domains. This solution structure shows greater resemblance to the crystal structures of homologous NusB proteins from ( 46 ) and ( 47 ). (B) Structure of NusE (S10) as part of a 30S ribosome particle (chain J of the coordinate available from PDB no. 1J5E) ( 48 ). The RNP fold of NusE may also be important for interacting with RNAP in the transcription EC.

Citation: Sen R, Chalissery J, Muteeb G. 2008. Nus Factors of , EcoSal Plus 2008; doi:10.1128/ecosalplus.4.5.3.1
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Figure 4

(A) Homology model of NusG ( 54 ), which is characterized by two globular domains, I and II, connected by a flexible linker. This linker most likely ensures degrees of freedom between the two domains and their respective orientations in the space. (B) Crystal structure of RfaH (PDB no. 2OUG) ( 58 ). The sequence of N-terminal domain I of RfaH is similar to that of domain I of NusG, and also the domain folds in a similar way as NusG domain I. The C-terminal domain II of RfaH is very different and folds into an α-helical coiled-coil structure, in contrast to the β-barrel structure of NusG, and comes over the domain I in the tertiary structure. Unlike domain II in NusG, in this conformation of RfaH, domain II blocks the access to domain I. (C) RfaH domain I is modeled onto the coiled-coil domain of the β subunit of RNAP, where it is shown that domain I is now unmasked from domain II of RfaH upon interaction with the EC. Different structural elements are indicated.

Citation: Sen R, Chalissery J, Muteeb G. 2008. Nus Factors of , EcoSal Plus 2008; doi:10.1128/ecosalplus.4.5.3.1
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Image of Figure 5
Figure 5

(A) Gene organization of early transcription region of lambdoid phages. Transcripts originating from P (left) and P (right) promoters get prematurely terminated at T (left) and T (right) terminators in the absence of N protein. N protein together with a battery of Nus factors recognizes the and elements of the RNA sites. The nature and sequences of these conserved elements from different lambdoid phages are depicted. Boxes (stem) and arrows (loop) indicate nucleotides corresponding to stem-loop structures. (B) Cartoon showing the assembly of an N antitermination complex on the site. Interactions of the NusB-NusE heterodimer with , the N terminus of N protein with , and N protein with the AR1 region of NusA have been experimentally verified. Other interaction sites in the complex have not been proven experimentally.

Fig. 5A is adapted from ( 107 ) with permission of the publisher.

Citation: Sen R, Chalissery J, Muteeb G. 2008. Nus Factors of , EcoSal Plus 2008; doi:10.1128/ecosalplus.4.5.3.1
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Image of Figure 6
Figure 6

(A) Typical organization of an rRNA operon corresponding to 16S, 23S, and 5S RNAs. The antitermination signals (AT) present in the leader and spacer regions are depicted. The major elements (--) recognized by the different components of the antitermination complex are shown. (B) Cartoon showing the assembly of different Nus factors and ribosomal proteins on the element of rRNA. Also shown is the transcription terminator Rho in the context of this antitermination complex. This complex helps the RNAP to overcome the Rho-dependent RNA release by increasing the elongation speed, by blocking the access of Rho, or by using both these mechanisms.

Citation: Sen R, Chalissery J, Muteeb G. 2008. Nus Factors of , EcoSal Plus 2008; doi:10.1128/ecosalplus.4.5.3.1
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Tables

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Table 1

Summary of different properties of the Nus factors

Citation: Sen R, Chalissery J, Muteeb G. 2008. Nus Factors of , EcoSal Plus 2008; doi:10.1128/ecosalplus.4.5.3.1

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