Table Of ContentInternational Journal of Applied
and Natural Sciences (IJANS)
ISSN (P): 2319–4014; ISSN (E): 2319–4022
Vol. 9, Issue 1, Dec-Jan 2020; 67–92
© IASET
RIBOSWITCH: AN AREA OF NOVEL BREAKTHROUGH IN RNA WORLD
Harpreet Kaur & Rajan Keshri
Research Scholar, Guru Arjan Dev Institute of Development Studies, Amritsar, India
ABSTRACT
Fundamentally, riboswitches are known to be highly structured and conserved metabolite binding domains, known to be
aptamer, which are locus within mRNAs. When we talk about RNA world, riboswitches are ranked among the trending
topics. Since its discovery from 2002, there is a large amount of feature disclosed till now and thanks to computational
analysis this finding are increasing every year with a fast rate. This work club up the information regarding new findings
within the field of riboswitches, which include data about its new classes discovery and its application in the field of gene
regulation mechanism, medical science, inter-cellular signalling, biosensors and many more.
KEYWORDS: Riboswitches, Discovery, Gene Regulation, Medical, Signalling, Biosensors
Article History
Received: 18 Dec 2019 | Revised: 27 Dec 2019 | Accepted: 13 Jan 2020
INTRODUCTION
Riboswitches are complex folded RNA domains that serve as receptors for specific metabolites. These domains are found
in the non-coding portions of various mRNAs, where they control gene expression by harnessing allosteric structural
changes that are brought about by metabolite binding. New findings indicate that riboswitches are robust genetic elements
that are involved in regulating fundamental metabolic processes in many organisms. (Mandal & Breaker, 2004)
Conceptually riboswitches are whole made of complicated and related folds of RNA domains, within certain mRNAs
that serve as precise demodulator or as receptors for ad hoc metabolites. Riboswitches were recognised for chip in to the
regulation of numerous fundamental metabolic pathways in certain bacteria which are found in the non-coding portions of
various mRNAs, where they control gene expression by adjusting allosteric structural changes that are brought about by
metabolite binding (Mandal et al., 2003; Mandal& Breaker, 2004). Riboswitches where detected to be expand in eubacteria, that
is, this system of modulation is among the most substantial mechanism by which metabolic genes are controlled. However, many
discoveries in the recent past of riboswitch categories have been depicting not only surprisingly complex mechanisms for
regulating gene expression but also new high-resolution structural models of these RNAs which also gives an insight into the
molecular details of metabolite recognition by natural RNA aptamer (Tucker & Breaker, 2005). RNA was always found to be
more affectionate stimuli in managing gene expression rather than it was thought to be (Lin he & Hannon, 2004; Erdmann et al.,
2001). It has been considered from long time that differential folding of RNA invests its concise contribution in transcriptional
attenuation (Henkin & Yanofsky 2002). In recent past there are novel discoveries of RNA-based regulatory mechanisms
admitting pathways involving antisense (Storz et al, 2004) and tRNA–mRNA interactions (Grundy & Henkin, 2003), control of
translation by temperature-dependent modulation of RNA structure (Chowdhury et al., 2003; Morita et al., 1999; Morita et al.,
1999b; Kamath & Gross., 1991) and the involvement of micro-RNAs as trans-acting genetic factors (Bartel, 2004).
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68 Harpreet Kaur & Rajan Keshri
The often-ness in which these breakthroughs have been erupting one after another signifies RNA has a crucial
relationship in cellular control processes. And this has been conformably proven to be true for bacteria, in recent findings
of gene control by riboswitches are revealing a distributive organization of RNA-mediated gene control (Winkler &
Breaker, 2003;Vitreschak, Rodionov, Mironov & Gelfand, 2004; Lai, 2003; Grundy & Henkin, 2004 and Brantl, 2004).
ORIGIN OF RIBOSWITCHES
Its starts with the discovery of the lac repressor (Gilbert & muller., 1966) a huge body of data came forth that described a
diversity of protein genetic factors that respond to various metabolites and signalling compounds. From that vast data of
scientific literature arise an event which represents the gene control phenomenon. Specifically scheming was a series of
reports that brought out the unique genetic-control characteristics of the btu B gene of Escherichia coli (Lawrence & Roth.,
1995) and the cob operon of Salmonella typhimurium (Roth et al., 1993). These genes are responsible for maintaining
adequate levels of coenzyme B12 in the cell either by importing or synthesizing this complex metabolite
The matter of Riboswitches beginning and evolution has made the study of RNA civilization very challenging. In
vitro choice of experimentation disclosed the proportional relief with which RNA could be developed to bind with specific
ligands, proposing that it takes a relatively very less time for natural selection to get transform into metabolite-binding
domains from RNA sequences. So, we can say that, narrowly distributed riboswitches may have come up late during the
course of evolutionary development. These types of cases might have given mount to independent classes of riboswitches
which are selective or specific to the similar compound, e.g., SAM (Corbino et al., 2005). The existence of TPP
riboswitches in all three kingdoms of life signifies the early inception of this riboswitch category. It is a matter of concern
that, at what stage of evolution could riboswitches has awakened? So, as per the RNA world hypothesis (Gilbert, 1986), at
certain point, RNA develop to behave as a catalyst of chemical reactions as well as a carrier of genetic information. The
catalytic potentiality of the glmS riboswitch-ribozyme and the power of riboswitches to act together with ‘‘ancient’’
coenzymes, such as, SAM, FMN or TPP which would have extended the former repertoire of biochemical reactions,
supply obliging causes to propose that riboswitch-like molecules were subservient for the origin and evolution of the
primordial RNA world (Breaker, 2006).
GENE-CONTROL MECHANISMS OF A RIBOSWITCH
In handling of coenzyme-B12 riboswitch, two major mode of gene control are obvious. At first stage regulation of RNA
transcription which includes the ligand –dependent formation of an intrinsic terminator stem. This Intrinsic terminator are
long stem-loop structure which are generally accompanied by a stretch of six or more U residues, which make RNA
polymerase to terminate transcription before the coding region of the mRNA is constructed (Gusarov & Nudler, 1999).
When the content of coenzyme B12 is not optimum, transcription of an mRNA which is linked with the coenzyme-B12
riboswitch generate a nascent mRNA which is in the aptamer domain remain uncomplicated with ligand. The detached
aptamer domain allows establishment of an ‘ANTI-TERMINATOR’ stem, which prevents establishment of the intrinsic
terminator stem and hence, allows transcription of the complete mRNA. However, when coenzyme-B12 content are
optimum, the nascent mRNA binds to a coenzyme-B12 molecule and the allosteric change in structure allows the intrinsic
terminator stem to generate. Transcription abortion results and gene expression is stopped as the coding region of the
mRNA is not constructed. As the only prof for this system with the coenzyme-B12 riboswitch comes from sequence
analysis (Vitreschak et al., 2003), leading observational proof for this mechanism exists for other riboswitch classes, (
Winkler, Nahvi,& Breaker., 2002; Winkle, Cohen-Chalamish, & Breaker, 2002; Mironov et al., 2002; Mandal, Boese,
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Riboswitch: An Area of Novel Breakthrough in RNA World 69
Barrick, Winkler,& Breaker, 2003;McDaniel, Grundy, Artsimovitch, & Henkin, 2003; Epshtein,, Mironov & Nudler, 2003
)The next mode of operandi that is practice by the coenzyme- B12 riboswitch functions at the stage of translation initiation.
As like allosteric changes in aptamer structure can control the establishment of intrinsic terminator and anti-terminator
stems, coenzyme-B12 binding causes structural changes in total stretch of mRNAs to assure access to the RIBOSOME-
BINDING SITE. Specifically, it is observed (Vitreschak, Rodionov, Mironov& Gelfand, 2003 ) that ribosomes are not fit
to construct steady, complexes with the btuB mRNA of E. coli when the coenzyme B12 is introduce, in an in vitro assay.
This monitoring matched, with sequence observed (Vitreschak, Rodionov, Mironov& Gelfand, 2003) andbiochemical
(Nahvi et al., 2004) proof for coenzyme-relying alternative folding by the btuB 5′-UTR, supports this process for gene
control. In uncommon instances, it seems that both transcription and translation can be controlled at the same time. This
can happen if the transcription-terminator stem is organized by involving base pairing with the ribosome binding site. This
collection of mechanisms would permit freshly start mRNA transcripts to be terminated by the terminator stem, whereas
transcripts whose formation had already authorized the point of transcription termination could feat the same structural
change to stop translation by jamming the ribosome-binding site. Further observational experiments are needed to be try
out whether this collection of mechanisms is surely employed by some riboswitches.
STRATEGY FOR THE BIOINFORMATICS ANALYSIS OF KNOWN RIBOSWITCH CLASSES
Riboswitches are generally utilized by bacteria in order to catch out a number of metabolites and ions to regulate gene
expression. Till now, about 40 different classes of riboswitches have been detected (McCown, Corbino, Stav, Sherlock
&Breaker, 2017), well-studied and observed and atomic resolution in complex with their connate ligands. The research
study caught its direction when the first discovery of riboswitch was witnessed in 2002, which has shown that these
noncoding RNA domains exploit many different structural features to construct binding pockets that are highly selective in
dealing with their target ligands. Many riboswitch classes are widely found in bacteria from nearly all lineages, whereas
others are extremely rare and found only a few species whose DNA has been sequenced. (Phillip et al., 2017).
Once settled, unanimity sequence and structural models used to describe every class of riboswitch (Ames &
Breaker, 2010). The unanimity model can also be fetched directly into bioinformatics algorithms in order to find out other
RNAs that closely match to the unanimity. These algorithms can be used to construct representatives such a “hits “over the
ground on how accurate their sequences and predicted substructures matched to the present consensus model. Outliers
which are presumed or proven to work as riboswitches can guide how the consensus model for the aptamer should be
modified to more accurately ponder the sequence and structural constraints on the riboswitch class. This bioinformatics
concept has been used several time in order to disclose the beingness of structural variants of preQ1- I, preQ1 -II, and
preQ1- III riboswitches (Phillip et al., 2017) and to disclose variants of guanine riboswitches that display changed ligand
particularities (Mandal &Breaker, 2007). Recent approach, of bioinformatics search criteria, have been used which was
directed by the known atomic-resolution structures of riboswitches, to recognised other rare variants whose ligand-binding
particularities have been changed or modified (Weinberg et al., 2017).
To analyse the sequence date they (Phillip et al., 2017) have used certain program. Initially, a program name
Infernal was used that searches sequence databases for new recruits of an RNA class by the method of comparative
sequence analysis (Eric Nawrocki &Eddy, 2013). Then they looked to describe more representatives by using RNAMotif
(Macke et al., 2001), that employees covariance model in a format as same as used by the previous program Infernal.
Hereafter, Infernal creates an extremely big sequence alignment files that were subjected to further manual and
computational analyses. Such as, RALEE was especially effective for aligning big RNA regions with many
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70 Harpreet Kaur & Rajan Keshri
representatives, which permit the recognition of conserved nucleotide sequences. R2R was helpful in computing rates of
covariation and conservation among nucleotides in each of the respective motif (Weinberg &Breaker, 2011). Moreover,
R2R was effective to make an overture graphic delineation of each individual motif, which was later on adapted to train
representations of consensus models.
More than 100,000 representatives of 38 formalised riboswitch classes had been reported by the computer-assisted
searches. In many cases it has being found, that the functions of recently detected variants can be deduced as their genomic
positions propose that they are regulating genes that are routinely linked with the members of the parent riboswitch class.
Still, it has been found that there are numerous members of a riboswitch class, experimental establishment of this
representatives either one or many, is commonly carried on only if the gene associations are unlike and when the structural
variation or sequence is significant. Common cases exist for the breakthrough of rare riboswitch versions with novel ligand
specificities that were hard to differentiate from the common members of a large riboswitch class. This trouble was found
for riboswitches like 2'-dG-I (Kim et al., 2008) and adenine (Mandal & Breaker, 2004) that are alike in structure and
sequence to guanine riboswitches. Likewise, riboswitches like 2'-dG-II (Weinberg et al., 2017) and c-AMP–GMP (Kellen
2'-berger et al,. 2015) classes stayed covered for decades until their parent classes had been detected. Hence, it is crucial to
remember that few bioinformatics hits allotted to a specific riboswitch class might actually stand for unestablished versions
that have modified ligand specificity.
SOME COMMON RIBOSWITCHES DISCOVERED
TPP
TPP riboswitch is the only riboswitch which is experimentally confirmed to be found in fungi, plant and algae among all
recently discovered 40 different classes of riboswitches. Its regulation system is found to be present in 15 oomycetes and
138 fungi. It is all being present in Basidiomycota and Ascomycota in ample amount where they are detected to regulate
biosynthesis of TPP or transporter genes. And most of the transporter genes were detected to have conserved domains
coherent urea, amino acid and nucleoside transporter gene families. The Genomic position of this Riboswitches when
related to the intron structure of the regulated gene, altered prediction of the exact regulation mechanism used by each
individual riboswitch.
TPP is a vitamin B1 derived coenzyme, which has its important in all shapes of life (Jurgenson, Begley, & Ealick,
2009). In archaea, algae, bacteria, plants and Fungi its synthesised de-novo (Cheah, Wachter, Sudarsan, & Breaker 2007)
(Croft, Moulin, Webb& Smith 2007) (Wachter, 2007) (McRose, D. et al 2014). Its aptamers are extremely conserved
throughout different lineages and among all other riboswitches classes it is most far-flung (McCown,, Corbino, Stav,
Sherlock,. & Breaker, 2017) (Sudarsan, Barrick, & Breaker, 2003). TPP riboswitch regulates gene expression in bacteria,
via control of transcription termination or translation initiation (Miranda-Ríos, Navarro, & Soberón, 2001) (Winkler,
Nahvi& Breaker, 2002) (Mironov, A. S. et al., 2002). whereas regulation of gene expression in eukaryotes is carried outvia
alternative splicing (Cheah, M. T, Wachter, A., Sudarsan, N. & Breaker, 2007) (Kubodera, T. et al. , 2003) (Li, S. &
Breaker, 2013). Splicing of the pre-mRNA started by rich TPP concentration and consequent activation of the riboswitch
leads to a short matured mRNA and non-functional protein product hence, forbidding the resultant steps in the TPP
biosynthesis pathway from happening. TPP riboswitches were experimentally formalised in some species of fungi where
they are required in regulate the expression and splicing of TPP biosynthesis (Cheah, Wachter, Sudarsan& Breaker , 2007)
(Kubodera, T. et al., 2003)and transporter (Li, S. & Breaker, 2013) genes. The recognition of new-fangled TPP
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Riboswitch: An Area of Novel Breakthrough in RNA World 71
riboswitches in fungi and associate species was delayed due to lack of application of computational tools and sampling bias
for new riboswitch detection. Still, the current JGI 1000 fungal genome project (Grigoriev, I. V. et al., 2014) has supplied
an ample content of fungal genome sequence data for various classes of fungi that can be mined to find extra illustrates of
fungal TPP riboswitches. To empathise the patterns of TPP riboswitch-based gene regulation in the fungal dynasty, it is
crucial to develop and study a proper picture of TPP riboswitch distribution throughout the presently known fungal species
data (Mukherjee et al., 2018).
AdoCbl
AdoCbl riboswitches are ample in all bacteria and generally control biosynthesis of associated enzymes and transporters at
the level of transcription termination and translation initiation (Winkler, Nahvi & Breaker, 2002). There are about 19 genes
detected to be distributed over four polycistronic messenger RNAs, in the ethanolamine utilization (eut) locus of
Enterococcus faecalis, which are appears to be regulated by an individual adenosyl cobalamine (AdoCbl)–responsive
riboswitch. AdoCbl-binding riboswitch is a component of a minor, trans-acting RNA, EutX, that furthermore holds a dual-
hairpin substrate for the RNA binding–response regulator, EutV. EutX employee this structure to attach EutV. EutV
acknowledged to regulate the eut messenger RNAs by binding dual-hairpin structures that convergence terminators and
thus stop transcription termination and this happens only in the absence of AdoCbl. In the other hand when AdoCbl is
found to be present, EutV cannot bind to EutX and, rather, induces transcriptional read through of multiple eut genes. This
function brings out riboswitch-mediated control of protein sequestration as a posttranscriptional mechanism to co-
ordinately regulate gene expression. (DebRoy et al., 2014).
SAM
S-adenosyl-L-methionine (SAM) is one of the crucial metabolite present in all living being, which is form by SAM
synthetase from the synthesis of ATP and methionine. SAM is also known by the name of universal methyl currency inside
the cells. In SAM the attachment of methyl group to the sulfonium ion is quite reactive and by application of
methyltransferases it can be easily channelized to substrates. And its maybe because of its necessity purpose in cell
metabolism, SAM is recognised as a most common riboswitch effector. Till now three different evolutionarily groups of
SAM riboswitches have been detected: the SAM-I superfamily (cited to as kindred in Rfam), comprising of the SAM-I (S-
box), SAM-IV, and SAM-I/IV families; the SAM-II superfamily, comprising of SAM-II and SAM-V families; and the
SAM-III (or SMK-box) family (Batey., 2011). The work on the SAM riboswitch families forms a effective primer to the
study of riboswitches and, to a level, to the whole structured RNAs.
The SAM-I super family
The Bacillus subtilis SAM-I (or S-box) riboswitch was the foremost SAM riboswitch family recognised and is among the
well-studied riboswitches. SAM-I was keyed out first in the genes of 5′ UTRs of sulfur metabolism which do not possess
any acknowledgeable transcription regulator binding sites (Grundy &Henkin, 1998) (Winkler, Nahvi, Sudarsan, Barrick
&Breaker, 2003). The SAM-I riboswitch family is commonly far-flung and its found generally in low-GC content
Grampositive bacteria (Gardner et al, 2011). SAM-I has various isoforms, and each individual isoform tuned to react
optimally to different ranges SAM concentration, which can be observed inside a single species. Such as, there are at least
eleven variants of SAM-I, within B. subtilis, and each individual variant tuned to regulate different genes (Winkler, Nahvi,
Sudarsan, Barrick &Breaker, 2003)(Tomsic, McDaniel, Grundy & Henkin, 2008). The riboswitches SAM-IV family was
detected within the genes of 5′-UTRs of sulfur metabolism in Actinomycetales (Weinberg et al, 2007). SAM-IV shares
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72 Harpreet Kaur & Rajan Keshri
various structural characters with SAM-I and hence, it can be counted in SAM-I superfamily. SAM-IV seems to bind SAM
in a similar manner to SAM-I, employing the interactions of same binding-site. A distinguishable family in the SAM-I
superfamily, “SAM-I/IV” was detected recently from metagenome sequences (Weinberg, Wang, Bogue, Yang, Corbino,
Moy &Breaker, 2010).
SAM-II super family
The “metA” motifs in αProteobacteria was the first SAM-II riboswitches to be detected. (Corbino et al., 2005). The pilot
detection, in Agrobacterium tumefaciens, were observed close to intrinsic transcription terminators; Still, the other cases
(admitting the crystal structure from a Sargasso Sea metagenome sequence) seems to sequester the Shine–Dalgarno
sequence (SD) (Gilbert, Rambo, Van Tyne &Batey, 2008).
These SAM-II riboswitches are a generally short sequence, that promotes the entire crystal structure, and instead
of an aptamer domain, it is found in complex with SAM (Gilbert, Rambo, Van Tyne &Batey, 2008). When SAM is bound,
SAM-II structure creates an H-type pseudoknot. The pseudoknot stops 2 nt upstream from the SD, but this seems to be
enough to block ribosome binding in the “off” state. The structurally associated riboswitches that is SAM-V is far-flung in
marine bacteria (Poiata, Meyer, Ames, Breaker, 2009). Like SAM-II, it seems to monitor expression chiefly by SD
sequestration. SAM-V anticipate binding site which is alike to that of SAMII. However, as in the case of SAM-I super
family, SAM-V distinguish from SAM-II in the peripheral area, beyond the SAM binding site.
SAM-III family
Finally, SAM-III riboswitch or we can say it the SMK-box, is also a translational riboswitch. SAM-III riboswitch was first
detected in the 5′-UTR of metK (SAM synthetase) in Lactobacillales (Fuchs, Grundy & Henkin, 2006) SAM-III riboswitch
can be commonly reported as three helices, at the crossway of which lay the SAM binding site. SAM-III, riboswitch also
closes up ribosome binding to the SD. SAM-III riboswitch SD sequence is instantly private as part of the SAM-bound
“off” state, in reality creating direct touches with SAM in the binding site (C. Lu &A.M. Smith, 2008). It can also happen
that translational riboswitches like SAM-II and SAM-III circuitously affect RNA constancy, since ribosomes act as a
protector by physically closing up the approach to the RNA by nucleases.
SAH
SAH riboswitches are linked genetically with genes for enzymes that demeanSAH to stop its toxic build-up and that
recycle constituents for the re-formation of SAM. Generally, SAM content is probably to be larger than SAH
concentrations, SAH riboswitches must powerfully separate against SAM. Surely, a representative SAH riboswitch comes
up to discriminate against SAM by roughly 1000 fold. This favoritism conceivably could be accomplished by shaping an
SAH binding pocket that makes a steric block of the additional methyl group on SAM (Breaker, R. R., 2012).
c-di-GMP
The character of bacteria to accommodate with their environment is highly crucial for their survival. The bis-(3'-5')-cyclic
dimeric guanosine monophosphate (c-di-GMP) signalling mechanism is a pathway that promotes bacteria to change their
characters in reaction to modification in environmental conditions (Hengge, 2009) (SchirmerT & J enal U , 2009) (Jenal U
&Malone J, 2008).There are about 500 plus detection of the c-di-GMP riboswitch have been observed inside many
bacterial genes of 5′ UTR, which includes the causative agents of cholera and anthrax (Sudarsan, N. et al., 2008). Coherent
with the noticed role of c-di-GMP in biological purpose, genes regulated by c-di-GMP riboswitches admit those needed in,
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Riboswitch: An Area of Novel Breakthrough in RNA World 73
chemotaxis sensing motility, pilus assembly and pathogenesis (Sudarsan, N. et al., 2008). As the c-di-GMP riboswitch
class binds c-di-GMP and regulates the expression of a large range of genes in reaction to binding to this second
messenger, it is awaited to be a primary downstream target in this signalling pathway and is the initial evidence of an RNA
involved in intracellular signalling (Sudarsan, N. et al., 2008). c-di-GMP–binding riboswitches are very crucial
downstream targets in the case of signalling pathway (Kathryn D Smith et al., 2009). The c-di-GMP riboswitch is the
foremost evidence of a gene-regulatory RNA that binds a second messenger (Kulshina et al., 2009).
The recognition of fresh classes of riboswitches, mRNA segments controlling gene expression, that binds to c-di-
GMP specifically, has brought out a totally new grade of regulation that calls for this dinucleotide (Lee, Baker, Weinberg ,
Sudarsan & Breaker, 2010) (Sudarsan et al., 2008).
Till now, two major classes of c-di-GMP have been detected which are, c-di-GMP I and II riboswitches,
respectively. They have been discovered in computational analysis and formalized experimentally. Crystallographic studies
of the c-di-GMP-bound aptamers have clarified the system of ligand binding and overall structures (Kulshina, Baird &
Ferre-D’Amare, 2009)(Smith KD et al., 2009)(Smith, Shanahan , Moore , Simon & Strobel, 2011) . As both the
riboswitches bind c-di-GMP asymmetrically so, it let to demand for somewhat alike molecular interactions, the structural
motifs and sequences of the RNA aptamers that adapt, c-di-GMP are quite dissimilar, indicating that they developed
independently. These regulatory motifs are most commonly employee and can take place in large numbers suggesting the
prime power of aptamer based c-di-GMP signalling (Sondermann et al., 2012).
Glycine
The Glycine riboswitches were foremost discovered in 2004 as a gene activator for the expression of GCV system
elements in Vibrio cholera and B. subtilis (Mandal M, Lee M et al., 2004). This riboswitch immediately ties up with
glycine that is present in ample amount, by utilizing evolutionarily preserved tandem sensing domains. Many riboswitches
act as repressors for transcription elongation,but glycine riboswitches works as gene activators that agitate the expression
of the GCV system elements (Mandal M, Lee M et al., 2004). Two Glycine Riboswitches Activate the Glycine Cleavage
System Essential for Glycine Detoxification in Streptomyces griseus; Takeaki Tezuka, Yasuo Ohnishi Department of
Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Jap.
An exemplum of these glycine-sensing RNAs group from Bacillus subtilis functions as an uncommon genetic on
shift for the gcvT operon, which codes for proteins that’s allows the formation of the glycine cleavage system. Many
glycine riboswitches incorporate two ligand-binding domains that work’s cooperatively to more intimately estimate a two-
state genetic switch. This progressed form of riboswitch may have developed to check that excessive glycine is
expeditiously utilised to give carbon flux through the citric acid cycle and monitor adequate concentration of the amino
acid for protein production.
A new analysis has been carried out of highly conserved RNA motifs in various bacterial species that have
characters as same as detected riboswitches (Jeffrey et al., 2004). Among those, one of the detected motifs, named gcvT is
observed in number of bacteria, where it is generally occupying upstream of genes that show protein elements of the
glycine cleavage system., a three-gene operon (gcvPA -gcvT-gcvPB) is described in B. subtilis that codes for elements of
this protein complex, which catalyses the foremost reactions for the utilization of glycine as an energy source (G. Kikuchi,
1973).
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74 Harpreet Kaur & Rajan Keshri
FMN
FMN (flavin mononucleotide) riboswitches are utilize by many bacteria to monitor the expression of genes responsible for
the transport and biosynthesis of this enzyme cofactor or its precursor, riboflavin. Some rare versions of FMN riboswitches
detected in the strains of Clostridium difficile (Blount KF, 2013) and some other bacteria generally monitor the expression
of proteins transporters and annotated as, involving multidrug efflux pumps. These RNAs no longer know FMN, and varies
from the original riboswitch unanimity sequence at nucleotide locations generally involved in tying of the phosphate and
ribityl mediatise of the cofactor. Representatives of one among the two version subtypes were observed to tie up with the
FMN riboflavin precursor and the degradation products FMN that is, lumichrome and lumiflavin (Ruben et al., 2019).
Riboswitches that tie up with flavin mononucleotide (FMN) constitute the 7th richest riboswitch class that has
been experimentally formalised till now (McCown et al. 2017). FAM riboswitch generally monitor the expression of genes
needed for the transport and biosynthesis of the coenzyme precursor riboflavin (Gelfand, Mironov, Jomantas , Kozlov &
Perumov, 1999). FMN and flavin adenine dinucleotide (FAD) are commonaly utilised as redox cofactors for flavoenzymes
involved in numerious expressions of cellular metabolism (Fischer & Bacher, 2005).
There are few families of archaeal and bacteria whose cellular system defend themselves from these dodecins
which constitutes as phototoxic components along with riboflavin-binding proteins. This dodecins act to both store of
riboflavin and forbid its unwanted breakdown (Grininger, Staudt , Johansson, Wachtveitl & Oesterhelt, 2009). By
reasonable assumption there are some bacterial species that also have remediation and detection systems in the case that
substantial content of FMN breakdown products gets collected.
Lysine
In bacteria, the intracellular concentration of several amino acids is controlled by riboswitches (Sudarsan, Wickiser,
Nakamura, Ebert& Breaker, 2003) (Grundy, Lehman & Henkin, 2003)(Rodionov, Vitreschak, Mironov & Gelfand, 2003)
(Mandal, M. et al., 2004). One of the important regulatory circuits involves lysine-specific riboswitches, which direct the
biosynthesis and transport of lysine and precursors common for lysine and other amino acids (Sudarsan, Wickiser,
Nakamura, Ebert, M. S. & Breaker, 2003) (Grundy, Lehman,& Henkin, 2003) (Rodionov, Vitreschak, Mironov, &
Gelfand, 2003).
This riboswitch are bacterial RNA structures that sense the amount of lysine and regulate the expression of lysine
transport and biosynthesis genes. This riboswitch class are generally observing in the 5’ untranslated region of messenger
RNAs, where they create extremely selective receptors for lysine. Lysine tie up to the receptor stabilizes an mRNA tertiary
structure that, in many events, tends to transcription termination prior to the next open reading frame can be expressed. A
lysine riboswitch possibly could be directed for antibacterial therapy by creating new compounds that tie up with the
riboswitch and inhibit lysine transport and biosynthesis genes. In certain test, it is identified that several lysine analogs that
tie up to riboswitches in vitro and stamp down Bacillus subtilis development, likely through a process of riboswitch-
mediated repression of lysine biosynthesis. This evidence suggested that riboswitches could act as fresh classes of
antibacterial drug targets (Kenneth et al., 2007).
c-di-AMP
The cyclic di-AMP (c-di-AMP) is a bacterial second messenger which is concerned in signalling cell wall stress and DNA
damage through interactions with various protein receptors and a far-flung ydaO-type riboswitch. (Ang Gao& Alexander
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Riboswitch: An Area of Novel Breakthrough in RNA World 75
Serganov, 2014)c-Di-AMP was first recognised on a structural study (Witte, Hartung, Buttner, K. & Hopfner, 2008) and
on further study it was observed in human pathogenic bacteria (Kamegaya, Kuroda,& Hayakawa, 2011) (Barker, J.R. et al.,
2013) (Corrigan, Abbott, Burhenne, Kaever & Grundling, 2011)and within the cytosol of host cells, after encroachment by
Listeria monocytogenes (Woodward, Iavarone,& Portnoy, 2010). c-Di-AMP is produce in reaction to unknown inputs from
two molecules of ATP and is felt by particular receptors (Corrigan, R.M. et al., 2013) that are going to affect numerous
cellular processes. c-di-AMP signalling demands an RNA motif observed in the 5′ UTR of the ydaO gene as a putative
riboswitch and this observed in many bacteria (Barrick, J.E. et al., 2004) This riboswitch was foremost proposed to react to
ATP (Watson, P.Y. & Fedor, 2012)and recently to c-di-AMP (Nelson, J.W. et al, 2013). ydaO motif are most
acknowledged riboswitches, as in numerous bacterial species they have over 3,000 representatives. The motif is found in
the locality of genes responsible for cell wall metabolism, transport and synthesis of sporulation, osmoprotectants, and
other crucial biological procedures (Barrick, J.E. et al., 2004)and hence, is predicted to either monitor different processes
or at least be responsibl in the monitoring of different reactions linked with these processes. Some of these cellular actions
use c-di-AMP signalling (Corrigan, R.M. & Grundling, 2013), indicating a key function of the riboswitch in c-di-AMP–
dependent gene expression control.
Fluoride
A riboswitch linked with crcB motif non-coding RNAs from Pseudomonas syringae has been detected that directs fluoride
ion with a Kd of about 60 mM and separates against otherhalogen ions (Baker, J. L. et al., 2012) This riboswitch generally
found in archaeal and bacterial species and was observed to start the expression of genes that encodeputative fluoride
transporters. Given the small size and negative charge of the fluoride ion, it seems remarkable that RNA can form a small
enough pocket to target it and discriminate against largerhalide ions.
Thermotoga petrophila fluoride riboswitch, that develop a higher-order RNA design braced by pseudoknot and
long-range reversed Watson–Crick and Hoogsteen ANU pair formation. The tie up fluoride ion is wrapped up within the
junctional design, grounded in place through direct classification to three Mg21 ions, which in turn are octahedrally
coordinated to water molecules and five inwardly pointing backbone phosphates. The structure of the fluoride riboswitch
in the tie up state demonstrates how RNA can create a binding pocket exclusive for fluoride, while incisive against larger
halide ions. The T. petrophila fluoride riboswitch likely works in gene regulation through a transcription termination
mechanism (Aiming Ren, Kanagalaghatta . Rajashankar& Dinshaw J. Patel, 2012).
PreQ1
The preQ1 riboswitch is a prominent part of riboswitches family that selectively detect purine and its relevant derivatives
(Meyer, Roth, Chervin, Garcia,& Breaker, 2008) (Weinberg, Z. et al., 2007). It’s also employee in the regulation of
queuosine (Q) transport and biosynthesis. The preQ1 is the final free precursor of prokaryote organism in the biosynthetic
pathway, prior to introductioninto the tRNA wobble location (Meier, Suter, Grosjean, Keith, & Kubli, 1985). However, the
regulation mechanism for the preQ1 riboswitch remains unclear. The NMR solution structure of preQ1 II riboswitch was
released in 2014 (pdb code: 2MIY)( Kang, M., Eichhorn, C. D. & Feigon, J. Structural determinants for ligand capture by a
class II preQ1 riboswitch. Proc. Natl. Acad. Sci. USA 111, E663–E671 (2014). ), which disclose the major practicality of
the planted hairpin for riboswitch in recognition of preQ1 (Wang et al., 2016).
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76 Harpreet Kaur & Rajan Keshri
Guanine
Riboswitches recently emerged as possible targets for the development of alternative antimicrobial approaches. Guanine-
sensing riboswitches in the bacterial pathogen Clostridioides difficile (formerly known as Clostridium difficile) constitute
potential targets based on them involvement in the regulation of basal metabolic control of purine compound. There are
four guanine riboswitches have been predicted in Clostridium difficile, to transcriptionally regulate several genes
responsible for biosynthesis of guanine monophosphate (GMP) or transport of related precursors (Monot et al., 2011) AS
uraA and pbuG are anticipated to encode an uracil and a purine permeate, respectively, xpt and guaA comprise of a
xanthine phosphoribosyl transferase and GMP synthase, respectively, and would be responsible for transition of precursor
metabolites into GMP. When of guanine fail to be present, the guanine riboswitch starts the shaping of an anti-terminator
element heading to downstream transcription. Whereas the presence of guanine accelerates the creation of a terminator
element checking premature transcription termination (Lok-HangYanab & AntoineLe Roux, 2018).
ZTP
The bacterial alarm one 5-aminoimidazole-4-carboxamide riboside 5′-triphosphate (AICAR triphosphate also called ZTP),
deduced from the monophosphorylated purine precursor ZMP, collects during folate absence. ZTP regulates genes
demanded in folate metabolism and purine through a cognate riboswitch. The crystal structure of the Fusobacterium
ulcerans riboswitch tie up to ZMP, which pairs the two subdomains whose port also constitutes a pseudoknot and ribose
zipper. The riboswitch detects the carboxamide oxygen of ZMP by a new inner-sphere coordination with a Mg2+ ion. The
ZTP riboswitch establishes that how particular small-molecule attaching can cause gathering of distant noncoding-RNA
domains to regulate gene expression (Christopher P Jones & Adrian R Ferré-D’Amaré, 2015).
A riboswitch in the pfl operon was observed to be the cellular means for detecting collection of Z nucleotides
(Kim, Nelson & Breaker, 2015). ZMP and ZTP were presented to tie to a conserved noncoding element of pfl mRNA
transcripts from different bacterial species that works as genetic ‘on switches’, transcription-promoting riboswitches, when
attached to ZMP or ZTP.
THF
Folic acid one of the crucial micronutrient which act as a key element in one-carbon metabolism. Tetrahydrofolate (THF)
in its reduced form, work as a carrier of one-carbon units in the form of formyl, methylene, or methyl groups that are
employee in purine, thymidine, and methionine biosynthesis, respectively (Bermingham & Derrick, 2002) De novo THF
biogenesis begins from GTP and continues in seven successive levels (de Cre´ cy-Lagard,Yacoubi.,Garza, Noiriel,, &
Hanson, 2007). Alternatively, Gram-positive bacteria scavenge folate from its surrounding by using a unique energy-
coupling factor (ECF) transport system made of a folate-binding protein (FolT) and a simple ECF module (Rodionov et al.,
2009). The detected riboswitch nominee is predicted to control expression of folT in number of Firmicutes, admitting
Lactobacillus species which are auxotrophic for folate. There is an evidence, happening in Ruminococcus obeum, in which
the RNA motif is linked with the folate biosynthesis folEQPBK operon (Ames, Rodionov, Weinberg, & Breaker, 2010).
The detection of a riboswitch class for folate derivatives serves us to disclose how cells feel and react by the
alteration of concentrations of these compounds. Folate metabolism enzymes presently act as a prime material for
antibacterial drug targets, and the localisation of THF riboswitches with coding locations of strange function may promotes
researchers to recognise more genes whose protein synthesis take part in folate metabolism. Moreover, THF riboswitches
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