RNA function would potentially explain the pleiotropic nature of

RNA
helicases classification- Most of the RNA helicases belong to the superfamily 2
(SF2) subclass of helicases that are characterized by sequence homology within
a helicase domain consisting of eight or nine conserved amino acid motifs (3).
SF2 consists of three subfamilies, termed DEAD, DEAH and DExH/D, based on
variations within a common DEAD (Asp-Glu-Ala- Asp) motif. (5)

 

RNA helicases in stress- Biochemically, RNA
helicases unwind double-stranded RNA (dsRNA) and thereby affects the
rearrangement of RNA secondary structure, which is associated with activation
of RNA function. DEAD-box RNA helicases are often present in RNA degradosome
complex, helping unwind the secondary structures to facilitate degradation (6).
Cells experience a range of stress conditions that leads to decrease in
cellular fitness, it may be biotic or abiotic. Bacteria in their natural
habitats encounter with various abiotic stress, and it follows that for altered
environmental conditions, RNA helicase activity may be required for cellular
adaptation (7).

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Cold induced
RNA helicases- Whole – genome scale transcription
analysis (8) tells the list of genes that are induced by cold stress. Under
short exposures to low temperatures on bacteria one can witness the primary
events in the patterns of gene transcription. Microarray expression data (9) shows
that many genes are induced by cold with high induction factor. These genes may
be grouped into functional categories like signal perception and transduction,
respiration and photosynthesis, transcription and translation, cell wall and
membrane maintenance, with various cellular functions and unknown functions.

 

Induction of RNA helicase expression
in response to a reduction in growth temperature intimates that RNA helicase
activity is required for normal cellular function at cold conditions. The reason
for this is unknown but it is generally assumed that helicase activity resolves
RNA secondary structures that are thermodynamically stabilized at low
temperature (10). This general function would potentially explain the
pleiotropic nature of cellular processes associated with cold-induced RNA
helicase inactivation.

 

Resolving the secondary structure of
RNA is not possible at long ranges, as many DEAD box RNA helicases are not
processive but unwinding of RNA duplexes can occur for short regions that
contains less than two helical turns invitro and protein cofactors or RNA
substrates enhance the processivity invivo (11).

 

Diversity- The expression of RNA helicases has been studied in various
bacteria like gram-negative, gram positive and archeal sp. These findings have
originated from transcriptomic or proteomic analysis. The genes encoding for
DEAD-box RNA helicases are 26 in Saccharomyces cerevisiae (12), 37 in human genome, of which at least
2 genes (DED1 and DBP2) are temperature regulated in yeast. DEAD- box RNA
helicase that is identical to that of Saccharomyces is found in a free-
living eukaryote Ashbyz gosypii, which is a fungus (13). Each RNA
helicase performs a specific function in case of eukaryotes. This is not
possible in prokaryotes because the genome encodes many RNA helicase genes and
the individual proteins participate in divergent pathways (14).

 

 

RNA helicase
gene complement- The gene complement of RNA helicase
of an organism is not associated with a free-living growth style. In free –
living obligate photoautotrophic cyanobacteria, low temperature induction of
RNA helicase expression has been observed. In Anabaena, crhC, one of the two DEAD- box RNA helicase genes,
specifically expresses only during temperature stress, induced by a temperature
downshift from 30 to 20oC (15). Invitro conditions, CrhC exhibits
limited RNA helicase activity and is localized to cell poles. This cellular
localization confirms that CrhC protein is associated with co-translational –
translocation of proteins into or across inner membrane. The other RNA helicase
gene crhB in Anabaena, resembles that of Synechocystis
RNA helicase crhR (16).

 

Synechocystis
genome encodes a single DEAD- box RNA helicase, crhR whose expression is
regulated by the electron transport chain redox status and it is stress
enhanced that increases reduction of chain, including temperature and salt
(17). The mutant cells that show a growth phenotype at 20oC on crhR
inactivation exhibits a pleiotropic effect, physiological and morphological
effects derived in a decrease in photosynthetic carbon fixation (18).

 

Inactivation of crhR produces
effects at all temperatures, which indicates that RNA helicase activity is
required constitutively even when the effects of mutation are exacerbated at
low temperature. CrhR is most closely related to DEAD, however the homology
encompasses only the core of RNA helicase, as CrhR has a unique C- terminal
extension which is specific to cyanobacterial genes only (19). This protein
domain may be related to the ability of CrhR to catalyse dsRNA unwinding,
annealing and strand exchange, which has the potential to perform RNA
structural rearrangements in addition to the other activities performed
generally by RNA helicases. In response to cold stress, CrhR activity
functionally has been associated with regulation of protein chaperone
expression, photosystem stoichiometry and various pathways. These genetics,
biochemical and structural aspects suggest that CrhR may perform a variety of
roles in Synechocystis RNA
metabolism.

 

Cold inducible expression of heat shock
genes groESL1 and groEL2, are regulated by CrhR (20). In the cyanobacteria Synechocystis, the groESL1 and groEL2 gene
expression is regulated by redox state of PQ pool (21). At initial periods of
low temperature incubation, repression of these genes was observed, and at
later stages upregulation in wild type cells was observed. This might suggest a
transient oxidation of reduced- PQ pool at low temperature incubation. A strong
repression of ?crhR cells was observed in contrast, which indicates the
oxidation of PQ pool at low temperatures (22).

 

Strong secondary structure mRNA
which are formed at low temperatures are unwound by CrhR, thus in absence of
CrhR some of the proteins cannot be expressed. The RNA helicase may facilitate
the translation of redox – regulated mRNA during acclimation at low
temperatures and thus maintain functional coordination between PSI and PSII at
low temperatures (19). The mRNA secondary structure may not be linearized in
absence of CrhR which might lead to inhibition of protein synthesis related to
these genes. An imbalance is created between photosystems resulting in an
oxidised PQ pool (23). This suggests the essentiality of CrhR for
photosynthetic acclimation at low temperatures.

 

Conclusions

 

In all organisms, RNA helicases are encoded, performing
important roles in cellular functions involving RNA metabolism. In a variety of
prokaryotic RNA pathways involved with abiotic stress, RNA helicases function. The
most studied stress is low temperature stress. At low temperatures, cyanobacteria
acclimate by adjusting their membranes, transcriptional and translational macheinaries
to protect all the functions occurring in the cell.

 

RNA
helicases also contribute to functional crosstalk between helicase and protein
cofactors. Thereby at changes in environmental conditions, they alter the
composition of functional protein complexes. Bacterial helicases may also
function in other cellular pathways contributing to the compartmentalization of
cellular function.