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Nucleotide sequence of a Mycoplasma mycoides RNA which is homologous to E. coli 4.5S RNA

Authors:
Tore Samuelsson at University of Gothenburg
Tore Samuelsson
Youssef Guindy
Youssef Guindy
Youssef Guindy
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4938
Nucleic
Acids
Research,
Vol.
18,
No.
16
Nucleotide
sequence
of
a
Mycoplasma
mycoides
RNA
which
is
homologous
to
E.
coli
4.5S
RNA
Tore
Samuelsson
and
Youssef
Guindy
Department
of
Medical
Biochemistry,
University
of
Goteborg,
PO
Box
33031,
S-40033
Goteborg,
Sweden
EMBL
accession
no.
X53678
We
have
previously
made
an
inventory
of
tRNAs
and
tRNA
genes
in
Mycoplasma
mycoides
(1-4)
and
in
the
course
of
this
investigation
we
discovered
another
RNA
which
was
approximately
the
size
of
a
tRNA.
It
was
purified
by
two-
dimensional
polyacrylamide
gel
electrophoresis
and
subjected
to
sequence
analysis
using
the
direct
read-out
method
of
Gupta
and
Randerath
(5).
A
gene
corresponding
to
this
RNA
was
also
isolated
by
screening
a
plasmid
library
of
EcoRI-fragments
of
M.
mycoides,
using
as
a
probe
32P-labeled
RNA.
The
nucleotide
sequence
of
the
gene
was
determined
and
is
shown
in
Fig.
1.
The
RNA
(77
nucleotides)
can
be
folded
into
a
hairpin
structure
as
indicated
in
Fig.
2
and
contains
a
structural
domain
typical
for
a
group
of
RNAs
that
include
the
4.5S
RNA
of
E.
coli,
scRNA
of
Bacillus
subtilis,
as
well
as
the
eukaryotic
SRP
RNAs
(6).
One
could
speculate
that
this
M.mycoides
RNA
is
functionally
analogous
to
the
4.5S
RNA
of
E.
coli
which
is
known
to
be
essential
for
viability
(7)
and
believed
to
be
important
for
efficient
translocation
during
protein
synthesis
in
vitro
(8).
REFERENCES
1.
Samuelsson,T.,
Elias,P.,
Lustig,F.
and
Guindy,Y.S.
(1985)
Biochem.
J.
232,
223-228.
2.
Samuelsson,T.,
Guindy,Y.S.,
Lustig,F.,
Boren,T.
and
Lagerkvist,U.
(1987)
Proc.
Natl.
Acad.
Sci.
USA
84,
3166-3170.
3.
Guindy,Y.S.,
Samuelsson,T.
and
Johansen,T.-I.
(1989)
Biochem.
J.
258,
869-873.
4.
Samuelsson,T.,
Boren,T.,
Johansen,T.-I.
and
Lustig,F.
(1988)
J.
Biol.
Chem.
263,
13692-13699.
5.
Gupta,R.C.
and
Randerath,R.
(1979)
Nucl.
Acids
Res.
6,
3443-3458.
6.
Portiz,M.A.,
Strub,K.
and
Walter,P.
(1988)
Cell
55,
4-6.
7.
Brown,S.
and
Fournier,M.J.
(1984)
J.
Mol.
Biol.
178,
533-550.
8.
Brown,S.
(1989)
J.
Mol.
Bio.
209,
79-90.
9.
Hsu,L.M.,
Zagorski,J.
and
Fournier,M.J.
(1984)
J.
Mol.
Bio.
178,
509-531.
1
ATTACAGCAT
AACGTGAATG
ATTATGTTTT
ATTAGGTGAT
TATAAAGATT
AATATCTACT
61
TAAttgaatA
AAACTTAAAA
ATATAAtata
atTATAACGC
CGCGATAAGA
ATAACATCTG
121
AACGAGTTAG
GACCGGAAGG
TAGCAGCTAT
AAGGAAAAGT
GTTCTGTATT
GCGGTTTTTT
181
ATTTGAAAAA
CTATGAGTGA
TTTTAATAAC
ATCTTAGATC
Figure
1.
The
nucleotide
sequence
of
a
M.
mycoides
gene
that
encodes
an
RNA
homologous
to
E.
coli
4.5S
RNA
and
other
related
RNAs.
The
sequence
corresponding
to
the
mature
RNA
is
underlined
and
putative
-10
and
-35
promoter
boxes
are
shown
in
lower
case
boldface
letters.
1
A
A
GCCGCGAUA
AGAAU
AC
UCU
:1111:111
1111:
11
11:
UGGCGUUAU
UCUUG
UG
AGG
77
G
A
A
A
G
G
^
AGUU
ACC
11:1
III
UC
UGG
(
A
U
G
Figure
2.
A
secondary
structure
model
for
the
RNA
encode
by
the
gene
in
Fig.
1.
The
E.
coli
4.5S
RNA
and
its
relatives
in
prokaryotes
and
archaebacteria
as
well
as
the
eukaryotic
SRP
RNAs
have
a
well
conserved
domain
in
common
(6).
The
Mycoplasma
RNA
possess
all
the
consensus
features
of
this
domain.
These
include
the
nucleotides
that
are
encircled
in
the
figure
as
well
as
the
particular
base
pairing
pattern
in
the
right
part
of
the
structure.
Indicated
in
bold
letters
are
the
nucleotides
that
are
identical
in
the
4.5S
RNA
of
E.
coli
(9).
Submitted
June
15,
1990
.n/
1990
Oxford
University
Press

Supplementary resource (1)

M.mycoides 4.5S RNA gene
Nucleotide Sequence
July 1990
Tore Samuelsson
... (29), and the remainder were derived on the basis of information in the original paper describing each RNA. References: S.solfataricus (47); T.thermophilus (36), and M.mycoides (34). ...
... The core structure of SRP is conserved through evolution. Notably, a structure homologous to domain IV of mammalian 7SL is present in both the highly truncated SRP-like RNA from M.mycoides (34) and in the much larger S.cerevisiae scRl RNA (this work). The ubiquity of the domain IV structure, together with the presence of conserved nucleotides (Figure 3), implies that it constitutes the essential RNA core of signal recognition particle. ...
Molecular evolution of SRP cycle components: Functional implications
Article
  • Jul 1994
Signal recognition particle (SRP) is a cytoplasmic ribonucleoprotein that targets a subset of nascent presecretory proteins to the endoplasmic reticulum membrane. We have considered the SRP cycle from the perspective of molecular evolution, using recently determined sequences of genes or cDNAs encoding homologs of SRP (7SL) RNA, the Srp54 protein (Srp54p), and the alpha subunit of the SRP receptor (SR alpha) from a broad spectrum of organisms, together with the remaining five polypeptides of mammalian SRP. Our analysis provides insight into the significance of structural variation in SRP RNA and identifies novel conserved motifs in protein components of this pathway. The lack of congruence between an established phylogenetic tree and size variation in 7SL homologs implies the occurrence of several independent events that eliminated more than half the sequence content of this RNA during bacterial evolution. The apparently non-essential structures are domain I, a tRNA-like element that is constant in archaea, varies in size among eucaryotes, and is generally missing in bacteria, and domain III, a tightly base-paired hairpin that is present in all eucaryotic and archeal SRP RNAs but is invariably absent in bacteria. Based on both structural and functional considerations, we propose that the conserved core of SRP consists minimally of the 54 kDa signal sequence-binding protein complexed with the loosely base-paired domain IV helix of SRP RNA, and is also likely to contain a homolog of the Srp68 protein. Comparative sequence analysis of the methionine-rich M domains from a diverse array of Srp54p homologs reveals an extended region of amino acid identity that resembles a recently identified RNA recognition motif. Multiple sequence alignment of the G domains of Srp54p and SR alpha homologs indicates that these two polypeptides exhibit significant similarity even outside the four GTPase consensus motifs, including a block of nine contiguous amino acids in a location analogous to the binding site of the guanine nucleotide dissociation stimulator (GDS) for E. coli EF-Tu. The conservation of this sequence, in combination with the results of earlier genetic and biochemical studies of the SRP cycle, leads us to hypothesize that a component of the Srp68/72p heterodimer serves as the GDS for both Srp54p and SR alpha. Using an iterative alignment procedure, we demonstrate similarity between Srp68p and sequence motifs conserved among GDS proteins for small Ras-related GTPases. The conservation of SRP cycle components in organisms from all three major branches of the phylogenetic tree suggests that this pathway for protein export is of ancient evolutionary origin.
View
... Recently, a minor small RNA, msr, showing some similarity with the 4.5S RNA of E. coli, has been identified in both M. mycoides and M. capricolum (24,25). The cloned M. mycoides msr gene was used as probe, and found to hybridize to fragments ApF, BsB, SIA and SmE, and, consequently, to be located in the vicinity of rmn. ...
A physical and genetic map of the Spiroplasma citri genome
Article
Full-text available
  • May 1992
A physical and genetic map of the Spiroplasma citri genome has been constructed using several restriction enzymes and pulsed field gel electrophoresis. A number of genes were subsequently localized on the map by the use of appropriate probes. The genome size of the spiroplasma estimated from restriction fragments is close to 1780 kbp, the largest of all Mollicutes studied so far. It contains multisite insertions of Spiroplasma virus 1 (SpV1) sequences. The physical and genetic map of the S. citri genome shares several features with that of other Mollicutes, especially those in the Mycoplasma mycoides cluster. This supports the finding that S. citri and these Mycoplasma spp. are phylogenetically related.
View
... The demonstration of a gene for a 4.5S RNA homolog in M. pneumoniae indicates the ubiquitous nature of this gene; it has been reported previously for bacteria (6,7,24), Schizosaccharomyces pombe (2), and humans (18,19). Recently, a small RNA bearing structural similarity to E. coli 4.5S RNA was described for Mycoplasma mycoides (20), although no functional studies were done. The relatively small size of the 4.5S RNA from M. pneumoniae (79 nucleotides) and its ability to complement the growth of the deficient strains of E. coli indicate that the essential function of E. coli 4.5S RNA (114 nucleotides) can be satisfied by a smaller molecule whose sequence similarity is restricted mainly to the hairpin end of the RNA. ...
The gene for a 4.5S RNA homolog from Mycoplasma pneumoniae: Genetic selection, sequence, and transcription analysis
Article
Full-text available
  • Feb 1992
In an effort to make an inventory of the tRNA genes of Mycoplasma pneumoniae, a DNA fragment was found to contain a sequence that can be folded into a hairpin structure very similar to that of the 4.5S RNA of Escherichia coli. Recombinant plasmids carrying this region were able to complement E. coli strains that were deficient in 4.5S RNA. S1 mapping showed that the mature transcript is only 79 nucleotides long.
View
Molecular Biology of Spiroplasmas: 1991
Chapter
  • Jan 1993
An extensive review of the molecular and cellular biology of spiroplasmas has been published in 1989 (Bové et al., 1989). The purpose of the present chapter is to update the 1989 review.
View
A Mycoplasma protein homologous to mammalian SRP54 recognizes a highly conserved domain of SRP RNA
Article
Full-text available
  • Dec 1992
A protein homologous to SRP54, a subunit of the mammalian signal recognition particle (SRP), was identified in Mycoplasma mycoides. The mycoplasma protein was expressed in E.coli and purified to near homogeneity. It was shown to bind specifically in vitro to a small mycoplasma RNA with structural features related to the RNA component of SRP. These findings provide evidence of a ribonucleoprotein complex in mycoplasma reminiscent of SRP. A part of the RNA was protected from ribonuclease digestion in the presence of the SRP54 homologue. The protected region contains structural elements that have been highly conserved in SRP RNAs durinq evolution.
View
View
Structural requirements of Bacillus subtilis small cytoplasmic RNA for cell growth, sporulation, and extracellular enzyme production
Article
  • Feb 1994
Bacillus subtilis small cytoplasmic RNA (scRNA; 271 nucleotides) is a member of the signal recognition particle (SRP) RNA family, which has evolutionarily conserved primary and secondary structures. The scRNA consists of three domains corresponding to domains I, II, and IV of human SRP 7S RNA. To identify the structural determinants required for its function, we constructed mutant scRNAs in which individual domains or conserved nucleotides were deleted, and their importance was assayed in vivo. The results demonstrated that domain IV of scRNA is necessary to maintain cell viability. On the other hand, domains I and II were not essential for vegetative growth but were preferentially required for the RNA to achieve its active structure, and assembled ribonucleoprotein between Ffh and scRNA is required for sporulation to proceed. This view is highly consistent with the fact that the presence of domains I and II is restricted to sporeforming B. subtilis scRNA among eubacterial SRP RNA-like RNAs.
View
The GTPase activity of the Escherichia coli Ffh protein is important for normal growth
Article
  • Jul 1995
  • Biochim Biophys Acta
The Escherichia coli (E. coli) Ffh protein is homologous to the 54kDa subunit of the eukaryotic signal recognition particle. We have examined an intrinsic GTPase activity of this protein and have created mutations in one sequence motif (GXXXXGK) of the putative GTP binding site. When glycine-112 was changed to valine (Ffh-G112V), Vmax was reduced to only 4% of the wildtype level. On the other hand, when glutamine-109 was altered to glycine (Ffh-Q109G), the major effect was a 50-fold increase in Km. These results show that the residues Q-109 and G-112 are essential for the binding and hydrolysis of GTP and that they are part of a catalytic site structurally related to that of many other GTPase proteins. Expression of the mutant protein Ffh-G112V in E. coli was highly toxic in the presence of the wildtype protein. In contrast, genetic complementation experiments showed that a viable strain could be constructed where the Ffh-Q109G mutant protein replaced wildtype Ffh. However, expression of the mutant protein had a negative effect on growth rate at 30 degrees C and resulted in elongated cells. These results demonstrate that the GTPase activity of the Ffh protein is required for proper function of the protein in vivo.
View
A small RNA of Mycoplasma capricolum that resembles eukaryotic U6 small nuclear RNA
Article
Full-text available
  • Jul 1993
Mycoplasma capricolum, a parasitic prokaryote, contains several small stable RNAs, besides rRNAs and tRNAs. One of them, designated MCS4 RNA (125 nucleotides in length), has been isolated and sequenced. This RNA is abundant in the cell, and is encoded by two genes. Unexpectedly, MCS4 RNA has been found to reveal extensive sequence similarity to eukaryotic U6 snRNAs. This finding suggests that MCS4 and U6 snRNAs are derived from a common ancestral RNA that has existed before the divergence of prokaryotes and eukaryotes.
View
GTPase activity of a bacterial SRP-like complex
Article
Full-text available
  • Mar 1993
We have recently identified a protein (SRPM54) in Mycoplasma mycoides homologous to SRP54, a subunit of the mammalian signal recognition particle (SRP). This protein forms a complex with a mycoplasma RNA related to the RNA component of SRP. We have now demonstrated that the protein has an intrinsic GTPase activity in vitro and kinetic parameters for the enzymatic reaction have been determined. The GTPase activity was not significantly affected by the presence of the mycoplasma SRP RNA. Different regions of the SRPM54 protein were expressed as recombinant proteins in E.coli and were purified to near homogeneity. On the basis of the properties of these SRPM54 fragments two different functional domains of the protein could be distuingished. An N-terminal part was found to contain the GTPase activity and this domain had approximately the same kinetic properties as the full-length protein. Another domain corresponding to a C-terminal fragment contained the RNA binding activity as shown using an assay based on the retention of RNA-protein complexes to nitrocellulose filters.
View
Unconventional codon reading by Mycoplasma mycoides tRNAs as revealed by partial sequence analysis
Article
Full-text available
  • Apr 1989
Continuing our investigation of the tRNA genes and gene products in Mycoplasma mycoides, we report the sequence of the gene for tRNALeu (CAA) as well as partial primary structures of the following tRNAs: Leu (CAA), Leu (UAG), Arg (UCU), Thr (AGU) and Ile (CAU). It is suggested that in M. mycoides, at least some of the family codon boxes are read by only one tRNA each, using an unconventional method which does not discriminate between the nucleotides in the third codon position. M. mycoides is the first free-living organism known to use an unconventional method of this kind.
View
Properties of a transfer RNA lacking modified nucleosides
Article
Full-text available
  • Oct 1988
A transfer RNA complete devoid of modified nucleosides was synthesized by in vitro transcription, and some of its properties in aminoacylation and protein synthesis in vitro were studied. For this purpose, a plasmid was constructed which contained a glycine tRNA gene from Mycoplasma mycoides under the promoter of the T7 RNA polymerase, as well as a BstNI restriction site at the 3'-end of the tRNA gene. Cleavage of plasmid DNA with BstNI followed by T7 RNA polymerase transcription in vitro yielded an RNA which was processed with M1 RNA, the catalytic subunit of ribonuclease P, to give a tRNA of mature length. The tRNA synthesized in this manner can be esterified with glycine in vitro, and the rate of aminoacylation is the same as when using the corresponding fully modified glycine tRNA from M. mycoides. Furthermore, in protein synthesis in vitro, the tRNA lacking modified nucleosides was essentially as efficient as the corresponding normal glycine tRNA. However, the Escherichia coli extract used in our protein-synthesizing system introduced one modification, pseudouridine, into the in vitro-synthesized tRNA, and it cannot be excluded that this modification has an essential role in protein synthesis.
View
Apparent lack of discrimination in the reading of certain codons in Mycoplasma mycoides
Article
Full-text available
  • Jun 1987
We report a cluster of four tRNA genes from Mycoplasma mycoides as well as the sequence of the alanine, proline, and valine tRNAs and the serine tRNA reading the UCN codons (where N stands for G, A, C, or U). This brings the total number of tRNA genes that we have so far characterized in this organism to 14, 6 of which code for tRNAs that read the codons of family boxes. In each of these latter cases, we found only one gene per family box, and the gene sequence contains a thymidine in the position corresponding to the wobble nucleotide, with the exception of the arginine tRNA gene that has an adenosine in this position. Furthermore, all of the tRNA structures reported here have an unsubstituted uridine in the wobble position. These findings are similar to those reported for mitochondria, especially yeast mitochondria, that contain an arginine tRNA with the anticodon ACG. However, the resemblance is not complete since we have demonstrated the presence of two isoacceptor tRNAs for threonine having uridine and adenosine, respectively, in the wobble position. It is suggested that in the M. mycoides at least some of the family codon boxes are read by only one tRNA each, using an unconventional method without discrimination between the nucleotides in the third codon position.
View
Cloning and nucleotide sequence analysis of transfer RNA genes from Mycoplasma mycoides
Article
Full-text available
  • Dec 1985
As part of an investigation of the tRNA genes of Mycoplasma mycoides, two HindIII fragments of mycoplasma DNA comprising 0.4 and 2.5 kilobases (kb), respectively, were cloned in pBR322 and their nucleotide sequences determined. Only one tRNA gene was found in the 0.4 kb fragment, the gene for tRNAArg with the anticodon TCT, while the 2.5 kb fragment contained nine different tRNA genes arranged in a cluster which presumably constitutes a transcriptional unit. The clustered tRNA genes, with their respective anticodons, were as follows: Arg (ACG), Pro (TGG), Ala (TGC), Met (CAT), Ile (CAT), Ser (TGA), fMet (CAT), Asp (GTC), and Phe (GAA).
View
Cloning and sequence analysis of the Escherichia coli 4.5 S RNA gene
Article
Full-text available
  • Oct 1984
The structure of the Escherichia coli gene coding for the metabolically stable 4.5 S RNA has been determined by cloning and DNA sequence analysis. Results from Southern hybridization assays carried out prior to cloning show the 4.5 S DNA to be limited to a single locus in the E. coli K12 genome. A 5.4 X 10(3) base DNA fragment containing the 4.5 S DNA was cloned into plasmid pBR322 for restriction, hybridization and sequence analyses. Cells harboring the cloned gene overproduce the 4.5 S RNA by 15-fold under normal culturing conditions; however, no effect on growth rate is observed. DNA sequencing revealed only one copy of the 4.5 S RNA gene, with a deduced RNA sequence both longer at 114 bases and slightly different from the RNA sequence reported earlier. A promoter structure immediately preceding the structural gene shows good agreement with the prokaryotic consensus sequence at both the -35 and -10 regions. In addition, a G + C-rich sequence between the Pribnow box and the start of transcription agrees well with an apparent consensus sequence found for other stable RNA genes also under stringent control. No clearly recognizable termination signal was found immediately downstream from the 3' terminus of the 4.5 S DNA, although structural elements with that potential appear to occur. A potential coding sequence for a protein occurs about 100 bases downstream from the 4.5 S DNA, suggesting the possibility of a dual function 4.5 S RNA-mRNA transcript.
View
Time of action of 4·5 S RNA in Escherichia coli translation
Article
  • Oct 1989
A new class of suppressor mutants helps to define the role of 4·5 S RNA in translation. The suppressors reduce the requirement for 4·5 S RNA by increasing the intracellular concentration of uncharged tRNA. Suppression probably occurs by prolonging the period in which translating ribosomes have translocated but not yet released the uncharged tRNA, indicating that this is the point at which 4·5 S RNA enters translation. The release of 4sd5 S RNA from polysomes is affected by antibiotics that inhibit protein synthesis. The antibiotic-sensitivity of this release indicates that 4·5 S RNA exits the ribosome following translocation and prior to release of protein synthesis elongation factor G. These results indicate that 4·5 S RNA acts immediately after ribosomal translocation. A model is proposed in which 4·5 S RNA stabilizes the post-translocation state by replacing 23 S ribosomal RNA as a binding site for elongation factor G. The 4·5 S RNA-requirement of mutants altered in 23 S ribosomal RNA support this model.
View
Rapid print-readout technique for sequencing of RNA's containing modified nucleotides
Article
  • Sep 1979
A rapid, simple, and highly sensitive method for sequence analysis of RNA was developed, which consists of the following steps: (i) controlled hydrolysis of the RNA by brief heating in water; (ii) (32P)-labeling of 5′-hydroxyl- groups of the fragments produced in (i); (iii) resolution of labeled fragments by size on polyacrylamide gels giving the familiar “ladder”; (iv) contact transfer (“print”) of the ladder from the gel to a PEI-cellulose thin layer; (v) in situ treatment of the ladder with RNase T2 resulting in the release of 5′-(32P)-labeled nucleoside-3′,5′ diphosphates; (vi) contact transfer and thin-layer separation of (32P)-labeled nucleotides on PEI-cellulose in ammonium sulfate and ammonium formate solvents; (vii) autoradiography. The chromatographic behavior of the 4 major and 18 modified nucleotides was determined, The positions of major and modified nucleotides in the sequence can be read directly from the separation patterns displayed on X-ray film. As this is the only sequencing method presently available that allows one to display and identify directly the positions in the RNA chain of major and modified nucleotides, no additional procedures are required to analyze the latter.
View
Human SRP RNA and E. coli 4.5S RNA contain a highly homologous structural domain
Article
  • Nov 1988
  • CELL
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The 4.5 S RNA gene of Escherichia coli is essential for cell growth
Article
  • Oct 1984
The Escherichia coli gene coding for the metabolically stable 4.5 S RNA (ffs) has been shown to be required for cell viability. Essentiality was demonstrated by examining the recombination behavior of substitution mutations of ffs generated in vitro. Substitution mutants of ffs are able to replace the chromosomal allele only in the presence of a second, intact copy of ffs. Independent evidence of essentiality and the finding that 4.5 S RNA is important for protein synthetic activity came from characterization of cells dependent on the lac operon inducer isopropyl-beta-D-thiogalactoside for ffs gene expression. Here, a strain dependent on isopropyl-beta-D-thiogalactoside for 4.5 S RNA synthesis was developed by inactivation of the chromosomal ffs allele and lysogenization by a lambda phage containing 4.5 S DNA fused to a hybrid trp-lac promoter. Withdrawal of the thiogalactoside leads to a deficiency in 4.5 S RNA, a dramatic loss in protein synthesis activity, and eventual cell death. Tagging of the chromosomal ffs region with a kanamycin-resistance gene allowed mapping of the 4.5 S RNA gene. Results from this analysis place ffs near lon at approximately ten minutes on the E. coli linkage map.
View
  • Jan 1979
  • 3443-3458
  • R C Gupta
  • R Randerath
Gupta,R.C. and Randerath,R. (1979) Nucl. Acids Res. 6, 3443-3458.