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EcoSal Plus

Domain 4:

Synthesis and Processing of Macromolecules

Nus Factors of

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
  • Authors: Ranjan Sen1, Jisha Chalissery2, M. Zuhaib Qayyum3, V. Vishalini4, and Ghazala Muteeb5
  • Editor: Susan T. Lovett6
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad 500001, India; 2: Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad 500001, India; 3: Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad 500001, India; 4: Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad 500001, India; 5: Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad 500001, India; 6: Department of Biology, Brandeis University, Waltham, MA
  • Received 08 July 2014 Accepted 10 October 2014 Published 21 November 2014
  • Address correspondence to Ranjan Sen, [email protected]
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  • Abstract:

    The highly conserved Nus factors of bacteria were discovered as essential host proteins for the growth of temperate phage λ in . Later, their essentiality and functions in transcription, translation, and, more recently, in DNA repair have been elucidated. Close involvement of these factors in various gene networks and circuits is also emerging from recent genomic studies. We have described a detailed overview of their biochemistry, structures, and various cellular functions, as well as their interactions with other macromolecules. Towards the end, we have envisaged different uncharted areas of studies with these factors, including their participation in pathogenicity.

  • Citation: Sen R, Chalissery J, Qayyum M, Vishalini V, Muteeb G. 2014. Nus Factors of , EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0008-2013

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This article is an updated version of the following content:
Nus Factors of

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/content/journal/ecosalplus/10.1128/ecosalplus.ESP-0008-2013
2014-11-21
2020-09-20

Abstract:

The highly conserved Nus factors of bacteria were discovered as essential host proteins for the growth of temperate phage λ in . Later, their essentiality and functions in transcription, translation, and, more recently, in DNA repair have been elucidated. Close involvement of these factors in various gene networks and circuits is also emerging from recent genomic studies. We have described a detailed overview of their biochemistry, structures, and various cellular functions, as well as their interactions with other macromolecules. Towards the end, we have envisaged different uncharted areas of studies with these factors, including their participation in pathogenicity.

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Nus Factors of
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Citation: Sen R, Chalissery J, Qayyum M, Vishalini V, Muteeb G. 2014. Nus Factors of , EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0008-2013
/content/ecosalplus/10.1128/ecosalplus.ESP-0008-2013.fig1
Figure 1

Positions of the respective genes are indicated in yellow. Directions of the arrows indicate the direction of transcription. Numbers at both sides indicate the nucleotide sequences. doi:10.1128/ecosalplus.ESP-0008-2013.f1

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Image of Figure 1
Figure 1

Positions of the respective genes are indicated in yellow. Directions of the arrows indicate the direction of transcription. Numbers at both sides indicate the nucleotide sequences. doi:10.1128/ecosalplus.ESP-0008-2013.f1

Citation: Sen R, Chalissery J, Qayyum M, Vishalini V, Muteeb G. 2014. Nus Factors of , EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0008-2013
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Figure 2

(A) A cartoon showing different functional domains of NusA. Domains NTD, SH, KH1/2 are highly conserved domains among different NusA molecules. Domains AR1/2 are found in few species, including . (B) Crystal structure of conserved domains of NusA from (Protein Data Bank [PDB] no. 1L2F [ 40 ]) depicts that each functional domain has distinct tertiary folds and corresponds to separate structural domains as indicated. Two separate NMR structures of AR1 and AR2 domains (PDB nos. 1WCL and 1WCN, respectively [ 36 ]) of are also shown. (C) Crystal structure of NusA (pink) with the stem-loop RNA (black) from boxC of rRNA operon (PDB no. 2ASB [ 32 ]). The structure revealed that both the RNA-binding domains KH1 and KH2 take part in the interaction with the RNA and the interaction destabilizes the stem-loop structure of boxC. (D) Solution structure of the central part of N protein (shown as a dark-green thread) from bacteriophage λ is complexed with the dimeric interface of AR1 domain of NusA (PDB no. 1U9L [ 33 ]). The dimeric interface was found to be formed from two AR1 domains coming from two NusA molecules; 352 to 419 residues of one NusA molecule (in maroon) dimerizes with the 352 to 421 residues of the second NusA molecule (light green). This indicates that, in the antitermination complex with λN, NusA may form a dimer. Amino acid numbers of the relevant region of λN protein are indicated. doi:10.1128/ecosalplus.ESP-0008-2013.f2

ecosalplus/6/1/ESP-0008-2013_fig_002_thmb.gif
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Figure 2

(A) A cartoon showing different functional domains of NusA. Domains NTD, SH, KH1/2 are highly conserved domains among different NusA molecules. Domains AR1/2 are found in few species, including . (B) Crystal structure of conserved domains of NusA from (Protein Data Bank [PDB] no. 1L2F [ 40 ]) depicts that each functional domain has distinct tertiary folds and corresponds to separate structural domains as indicated. Two separate NMR structures of AR1 and AR2 domains (PDB nos. 1WCL and 1WCN, respectively [ 36 ]) of are also shown. (C) Crystal structure of NusA (pink) with the stem-loop RNA (black) from boxC of rRNA operon (PDB no. 2ASB [ 32 ]). The structure revealed that both the RNA-binding domains KH1 and KH2 take part in the interaction with the RNA and the interaction destabilizes the stem-loop structure of boxC. (D) Solution structure of the central part of N protein (shown as a dark-green thread) from bacteriophage λ is complexed with the dimeric interface of AR1 domain of NusA (PDB no. 1U9L [ 33 ]). The dimeric interface was found to be formed from two AR1 domains coming from two NusA molecules; 352 to 419 residues of one NusA molecule (in maroon) dimerizes with the 352 to 421 residues of the second NusA molecule (light green). This indicates that, in the antitermination complex with λN, NusA may form a dimer. Amino acid numbers of the relevant region of λN protein are indicated. doi:10.1128/ecosalplus.ESP-0008-2013.f2

Citation: Sen R, Chalissery J, Qayyum M, Vishalini V, Muteeb G. 2014. Nus Factors of , EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0008-2013
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Figure 3

(A) Solution structure of NusB (PDB no. 1EY1 [ 42 ]) consisting of N- and C-terminal globular domains. This solution structure shows more resemblance with the crystal structures of homologous NusBs from ( 44 ) and ( 45 ). (B) Structure of NusE (S10) when it is a part of 30S ribosome particle (chain J of the co-ordinate available from PDB no. 1J5E [ 50 ]). The RNP fold of NusE may also be important for interacting with RNA polymerase in the transcription elongation complex. doi:10.1128/ecosalplus.ESP-0008-2013.f3

ecosalplus/6/1/ESP-0008-2013_fig_003_thmb.gif
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Figure 3

(A) Solution structure of NusB (PDB no. 1EY1 [ 42 ]) consisting of N- and C-terminal globular domains. This solution structure shows more resemblance with the crystal structures of homologous NusBs from ( 44 ) and ( 45 ). (B) Structure of NusE (S10) when it is a part of 30S ribosome particle (chain J of the co-ordinate available from PDB no. 1J5E [ 50 ]). The RNP fold of NusE may also be important for interacting with RNA polymerase in the transcription elongation complex. doi:10.1128/ecosalplus.ESP-0008-2013.f3

Citation: Sen R, Chalissery J, Qayyum M, Vishalini V, Muteeb G. 2014. Nus Factors of , EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0008-2013
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Figure 4

(A) Homology model of NusG ( 57 ), which is characterized by two globular domains NTD (PDB no. 2K06) and CTD (PDB no. 2JVV), 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 [ 67 ]). The sequence of NTD of RfaH is similar to that of NusG and folds in a similar way, whereas the CTD is very different: it folds into a α-helical coiled-coil structure, in contrast to the β-barrel structure of NusG, and comes over the NTD in the tertiary structure. Unlike NusG, in this conformation RfaH-CTD blocks the access of NTD. (C) Conversion of coiled-coil structure of RfaH-CTD into β-barrel structure; this transformation occurs upon interaction with EC. (D) Model of the RfaH NTD, unmasked from the CTD of RfaH, bound to the EC. Different structural elements are indicated. doi:10.1128/ecosalplus.ESP-0008-2013.f4

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Figure 4

(A) Homology model of NusG ( 57 ), which is characterized by two globular domains NTD (PDB no. 2K06) and CTD (PDB no. 2JVV), 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 [ 67 ]). The sequence of NTD of RfaH is similar to that of NusG and folds in a similar way, whereas the CTD is very different: it folds into a α-helical coiled-coil structure, in contrast to the β-barrel structure of NusG, and comes over the NTD in the tertiary structure. Unlike NusG, in this conformation RfaH-CTD blocks the access of NTD. (C) Conversion of coiled-coil structure of RfaH-CTD into β-barrel structure; this transformation occurs upon interaction with EC. (D) Model of the RfaH NTD, unmasked from the CTD of RfaH, bound to the EC. Different structural elements are indicated. doi:10.1128/ecosalplus.ESP-0008-2013.f4

Citation: Sen R, Chalissery J, Qayyum M, Vishalini V, Muteeb G. 2014. Nus Factors of , EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0008-2013
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Figure 5

(A) The gene organization of early transcription region of lambdoid phages. Transcripts originated from PL and PR promoters get prematurely terminated at T and T terminators in the absence of N protein. N protein together with a battery of Nus factors recognize the boxA and boxB elements of the RNA coded by sites. The nature and sequences of these conserved elements are described for different lambdoid phages (adapted from Figure 2 of reference 147 ). (B) A cartoon showing the assembly of N-antitermination complex on the site. Interactions of NusB/NusE heterodimer with boxA, N-terminal of N with BoxB, and N with AR1 region of NusA have been experimentally verified. Other interaction sites in the complex are not proven experimentally. doi:10.1128/ecosalplus.ESP-0008-2013.f5

ecosalplus/6/1/ESP-0008-2013_fig_005_thmb.gif
ecosalplus/6/1/ESP-0008-2013_fig_005.gif
Image of Figure 5
Figure 5

(A) The gene organization of early transcription region of lambdoid phages. Transcripts originated from PL and PR promoters get prematurely terminated at T and T terminators in the absence of N protein. N protein together with a battery of Nus factors recognize the boxA and boxB elements of the RNA coded by sites. The nature and sequences of these conserved elements are described for different lambdoid phages (adapted from Figure 2 of reference 147 ). (B) A cartoon showing the assembly of N-antitermination complex on the site. Interactions of NusB/NusE heterodimer with boxA, N-terminal of N with BoxB, and N with AR1 region of NusA have been experimentally verified. Other interaction sites in the complex are not proven experimentally. doi:10.1128/ecosalplus.ESP-0008-2013.f5

Citation: Sen R, Chalissery J, Qayyum M, Vishalini V, Muteeb G. 2014. Nus Factors of , EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0008-2013
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/content/ecosalplus/10.1128/ecosalplus.ESP-0008-2013.fig6
Figure 6

(A) Typical organization of an rRNA operon coding for 16S, 23S, and 5S RNAs. The antitermination signal (AT) present in the leader and spacer regions are described. The major elements (boxB-A-C) that are 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 boxA element of rRNA is described. Also shown is the transcription terminator Rho in the context of this antitermination complex. This complex helps the RNA polymerase to overcome the Rho-dependent RNA release either by increasing the elongation speed or by blocking the access of Rho, or by both the mechanisms doi:10.1128/ecosalplus.ESP-0008-2013.f6

ecosalplus/6/1/ESP-0008-2013_fig_006_thmb.gif
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Image of Figure 6
Figure 6

(A) Typical organization of an rRNA operon coding for 16S, 23S, and 5S RNAs. The antitermination signal (AT) present in the leader and spacer regions are described. The major elements (boxB-A-C) that are 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 boxA element of rRNA is described. Also shown is the transcription terminator Rho in the context of this antitermination complex. This complex helps the RNA polymerase to overcome the Rho-dependent RNA release either by increasing the elongation speed or by blocking the access of Rho, or by both the mechanisms doi:10.1128/ecosalplus.ESP-0008-2013.f6

Citation: Sen R, Chalissery J, Qayyum M, Vishalini V, Muteeb G. 2014. Nus Factors of , EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0008-2013
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Tables

Nus Factors of
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Citation: Sen R, Chalissery J, Qayyum M, Vishalini V, Muteeb G. 2014. Nus Factors of , EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0008-2013
/content/ecosalplus/10.1128/ecosalplus.ESP-0008-2013.T1
Table 1

Summary of different properties of Nus factors

Generic image for table
Table 1

Summary of different properties of Nus factors

Citation: Sen R, Chalissery J, Qayyum M, Vishalini V, Muteeb G. 2014. Nus Factors of , EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0008-2013

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