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Variation in the ribosome interacting loop of the Sec61α from Giardia lamblia.

Sinha A, Ray A, Ganguly S, Ghosh Dastidar S, Sarkar S - Biol. Direct (2015)

Bottom Line: The interaction between the ribosome and the endoplasmic reticulum-located Sec61 protein translocon is mediated through an arginine residue of Sec61α, which is conserved in all prokaryotic and eukaryotic orthologues characterized to date.Using in silico approaches we report that instead of arginine, this ribosome-interaction function is most likely discharged by a lysine residue in the protist Giardia lamblia.This functional substitution of the R with a K in GlSec61α may have taken place to accommodate a G-rich rRNA.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Bose Institute, P-1/12 CIT Road, Scheme VII M, Kolkata, 700054,, West Bengal, India. abhishek.boseinst.84@gmail.com.

ABSTRACT
The interaction between the ribosome and the endoplasmic reticulum-located Sec61 protein translocon is mediated through an arginine residue of Sec61α, which is conserved in all prokaryotic and eukaryotic orthologues characterized to date. Using in silico approaches we report that instead of arginine, this ribosome-interaction function is most likely discharged by a lysine residue in the protist Giardia lamblia. This functional substitution of the R with a K in GlSec61α may have taken place to accommodate a G-rich rRNA.

No MeSH data available.


Related in: MedlinePlus

a Sequence alignment of GlSec61α from G. lamblia Assemblage A isolate WB with orthologous sequences from S. cerevisiae, A. thaliana, H. sapiens, C. lupus, S. scrofa, C. hominis, P. falciparum, T. gondii, L. major, T. brucei, E. coli, M. jannaschii, T. thermophilus and P. furiosus. The secondary structure elements have been marked below the alignment, with spirals representing α-helices, arrows representing β-strands and lines representing intervening loops. Only the transmembrane helices have been numbered. The downward pointing red arrow marks the conserved arginine (R) required for interaction with ribosome while the functionally-equivalent lysine (K) residue in the putative GlSec61α has been highlighted with a black box. b Tertiary structure of a section of GlSec61α obtained by homology modeling based on 2WWB (i, ii and iii) and 3J7Q (iv, v and vi). Each of the homology modeled structures underwent molecular dynamic simulation for 30 ns, with (iii and vi) or without (ii and v) docked RNA. The side chains of residues K426 and E414 are shown. To indicate the orientation of the loop 8/9, two residues on either side of K426 have been marked (424-dark blue, 425-light blue, 427-amber and 428-red).
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Fig1: a Sequence alignment of GlSec61α from G. lamblia Assemblage A isolate WB with orthologous sequences from S. cerevisiae, A. thaliana, H. sapiens, C. lupus, S. scrofa, C. hominis, P. falciparum, T. gondii, L. major, T. brucei, E. coli, M. jannaschii, T. thermophilus and P. furiosus. The secondary structure elements have been marked below the alignment, with spirals representing α-helices, arrows representing β-strands and lines representing intervening loops. Only the transmembrane helices have been numbered. The downward pointing red arrow marks the conserved arginine (R) required for interaction with ribosome while the functionally-equivalent lysine (K) residue in the putative GlSec61α has been highlighted with a black box. b Tertiary structure of a section of GlSec61α obtained by homology modeling based on 2WWB (i, ii and iii) and 3J7Q (iv, v and vi). Each of the homology modeled structures underwent molecular dynamic simulation for 30 ns, with (iii and vi) or without (ii and v) docked RNA. The side chains of residues K426 and E414 are shown. To indicate the orientation of the loop 8/9, two residues on either side of K426 have been marked (424-dark blue, 425-light blue, 427-amber and 428-red).

Mentions: Although the sequences of Sec61α orthologues are extremely conserved, GlSec61α has low sequence identity (between 34.7 % and 55.5 %) with the orthologous sequences derived from evolutionarily diverse eukaryotes (Additional file 1). To ensure that this divergent sequence indeed represents the Sec61α orthologue, we determined its predicted secondary structure and observed that similar to all eukaryotic Sec61α and prokaryotic SecY, GlSec61α has the potential to form ten transmembrane helices (Fig. 1a) [3–6]. The sequence alignment shows that the span of each helix and also the spacing between adjoining helices of GlSec61α are similar to that of other orthologues. Additionally, both Phyre2 and PSIPRED predict the N-terminus of the GlSec61α to be in the cytoplasm, which is identical to the topology of the other orthologues. Therefore, although the sequence of GlSec61α is least conserved amongst all the orthologues considered in this study, secondary structure predictions indicate that it is likely to adopt a similar structure.Fig. 1


Variation in the ribosome interacting loop of the Sec61α from Giardia lamblia.

Sinha A, Ray A, Ganguly S, Ghosh Dastidar S, Sarkar S - Biol. Direct (2015)

a Sequence alignment of GlSec61α from G. lamblia Assemblage A isolate WB with orthologous sequences from S. cerevisiae, A. thaliana, H. sapiens, C. lupus, S. scrofa, C. hominis, P. falciparum, T. gondii, L. major, T. brucei, E. coli, M. jannaschii, T. thermophilus and P. furiosus. The secondary structure elements have been marked below the alignment, with spirals representing α-helices, arrows representing β-strands and lines representing intervening loops. Only the transmembrane helices have been numbered. The downward pointing red arrow marks the conserved arginine (R) required for interaction with ribosome while the functionally-equivalent lysine (K) residue in the putative GlSec61α has been highlighted with a black box. b Tertiary structure of a section of GlSec61α obtained by homology modeling based on 2WWB (i, ii and iii) and 3J7Q (iv, v and vi). Each of the homology modeled structures underwent molecular dynamic simulation for 30 ns, with (iii and vi) or without (ii and v) docked RNA. The side chains of residues K426 and E414 are shown. To indicate the orientation of the loop 8/9, two residues on either side of K426 have been marked (424-dark blue, 425-light blue, 427-amber and 428-red).
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Related In: Results  -  Collection

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Fig1: a Sequence alignment of GlSec61α from G. lamblia Assemblage A isolate WB with orthologous sequences from S. cerevisiae, A. thaliana, H. sapiens, C. lupus, S. scrofa, C. hominis, P. falciparum, T. gondii, L. major, T. brucei, E. coli, M. jannaschii, T. thermophilus and P. furiosus. The secondary structure elements have been marked below the alignment, with spirals representing α-helices, arrows representing β-strands and lines representing intervening loops. Only the transmembrane helices have been numbered. The downward pointing red arrow marks the conserved arginine (R) required for interaction with ribosome while the functionally-equivalent lysine (K) residue in the putative GlSec61α has been highlighted with a black box. b Tertiary structure of a section of GlSec61α obtained by homology modeling based on 2WWB (i, ii and iii) and 3J7Q (iv, v and vi). Each of the homology modeled structures underwent molecular dynamic simulation for 30 ns, with (iii and vi) or without (ii and v) docked RNA. The side chains of residues K426 and E414 are shown. To indicate the orientation of the loop 8/9, two residues on either side of K426 have been marked (424-dark blue, 425-light blue, 427-amber and 428-red).
Mentions: Although the sequences of Sec61α orthologues are extremely conserved, GlSec61α has low sequence identity (between 34.7 % and 55.5 %) with the orthologous sequences derived from evolutionarily diverse eukaryotes (Additional file 1). To ensure that this divergent sequence indeed represents the Sec61α orthologue, we determined its predicted secondary structure and observed that similar to all eukaryotic Sec61α and prokaryotic SecY, GlSec61α has the potential to form ten transmembrane helices (Fig. 1a) [3–6]. The sequence alignment shows that the span of each helix and also the spacing between adjoining helices of GlSec61α are similar to that of other orthologues. Additionally, both Phyre2 and PSIPRED predict the N-terminus of the GlSec61α to be in the cytoplasm, which is identical to the topology of the other orthologues. Therefore, although the sequence of GlSec61α is least conserved amongst all the orthologues considered in this study, secondary structure predictions indicate that it is likely to adopt a similar structure.Fig. 1

Bottom Line: The interaction between the ribosome and the endoplasmic reticulum-located Sec61 protein translocon is mediated through an arginine residue of Sec61α, which is conserved in all prokaryotic and eukaryotic orthologues characterized to date.Using in silico approaches we report that instead of arginine, this ribosome-interaction function is most likely discharged by a lysine residue in the protist Giardia lamblia.This functional substitution of the R with a K in GlSec61α may have taken place to accommodate a G-rich rRNA.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Bose Institute, P-1/12 CIT Road, Scheme VII M, Kolkata, 700054,, West Bengal, India. abhishek.boseinst.84@gmail.com.

ABSTRACT
The interaction between the ribosome and the endoplasmic reticulum-located Sec61 protein translocon is mediated through an arginine residue of Sec61α, which is conserved in all prokaryotic and eukaryotic orthologues characterized to date. Using in silico approaches we report that instead of arginine, this ribosome-interaction function is most likely discharged by a lysine residue in the protist Giardia lamblia. This functional substitution of the R with a K in GlSec61α may have taken place to accommodate a G-rich rRNA.

No MeSH data available.


Related in: MedlinePlus