The r factors of RNA polymerase play central roles when bacteria adapt to different environmental conditions. We studied heat-shock responses in the cyanobacterium Synechocystis sp. PCC6803 using the r factor inactivation strains DsigB, DsigD and DsigBD. The SigB factor was found to be important for short-term heat-shock responses and acquired thermotolerance. The normal high-temperature induction of the hspA gene depended on the SigB factor. The SigD r factor had a role in high-temperature responses as well, and the double inactivation strain DsigBD grew more slowly at 43°C than the DsigB and DsigD strains.

Cyanobacteria are eubacteria that perform oxygenic photosynthesis like plants. The initiation of transcription, mediated by the RNA polymerase holoenzyme, is the main determinant of gene regulation in eubacteria. The s factor of the RNA polymerase holoenzyme is responsible for the recognition of a promoter sequence. In the cyanobacterium Synechocystis sp. PCC 6803, the primary s factor, SigA, is essential for cell viability. The SigB, SigC, SigD, and SigE factors show significant sequence similarity with the SigA factor but are nonessential. In this study, we have used homology modeling to construct a three-dimensional model of Synechocystis RNA polymerase holoenzyme and all group 1 and 2 s factors. According to the models, the overall three-dimensional structures of group 1 and 2 s factors are similar, the SigB and SigD factors being the most similar ones. In addition, we have constructed a complete set of group 2 s factor double inactivation strains, DsigBC, DsigBD, DsigBE, DsigCD, DsigCE, and DsigDE. All double mutants grow well under standard conditions, but differences are observed in stress conditions. The transition from lag phase to exponential growth is slow in the DsigBD strain, and all strains lacking the SigD factor were found to be sensitive to bright light. Furthermore, all group 2 s factors were found to be involved in acclimation to salt-or sorbitol-induced osmotic stresses.

Changing of principal s factor in RNA polymerase holoenzyme to a group 2 s factor redirects transcription when cyanobacteria acclimate to suboptimal environmental conditions. The group 2 sigma factor SigB was found to be important for the growth of the cyanobacterium Synechocystis sp. PCC 6803 in high-salt (0.7 M NaCl) stress but not in mild heat stress at 43°C although the expression of the sigB gene was similarly highly, but only transiently up-regulated at both conditions. The SigB factor was found to regulate many salt acclimation processes. The amount of glucosylglycerol-phosphate synthase, a key enzyme in the production of the compatible solute glucosylglycerol, was lower in the inactivation strain DsigB than in the control strain. Addition of the compatible solute trehalose almost completely restored the growth of the DsigB strain at 0.7 M NaCl. High-salt conditions lowered the chlorophyll and phycobilin contents of the cells while protective carotenoid pigments, especially zeaxanthin and myxoxanthophyll, were up-regulated in the control strain. These carotenoids were up-regulated in the DsigCDE strain (SigB is the only functional group 2 s factor) and down-regulated in the DsigB strain under standard conditions. In addition, the HspA heat shock protein was less abundant and more abundant in the DsigB and DsigCDE strains, respectively, than in the control strain in high-salt conditions. Some cellular responses are common to heat and salt stresses, but pretreatment with mild heat did not protect cells against salt shock although protection against heat shock was evident.

Acclimation of cyanobacteria to environmental changes includes major changes in the gene expression patterns partly orchestrated by the replacement of a particular subunit with another in the RNA polymerase holoenzyme. The cyanobacterium Synechocystis sp. strain PCC 6803 encodes nine factors, all belonging to the 70 family. Cyanobacteria typically encode many group 2 factors that closely resemble the principal factor. We inactivated three out of the four group 2 factors of Synechocystis simultaneously in all possible combinations and found that all triple inactivation strains grow well under standard conditions. Unlike the other strains, the ⌬sigBCD strain, which contains SigE as the only functional group 2 factor, did not grow faster under mixotrophic than under autotrophic conditions. The SigB and SigD factors were important in lowtemperature acclimation, especially under diurnal light rhythm. The ⌬sigBCD, ⌬sigBCE, and ⌬sigBDE strains were sensitive to high-light-induced photoinhibition, indicating a central role of the SigB factor in high-light tolerance. Furthermore, the ⌬sigBCE strain (SigD is the only functional group 2 factor) appeared to be locked in the high-fluorescence state (state 1) and grew slowly in blue but not in orange or white light. Our results suggest that features of the triple inactivation strains can be categorized as (i) direct consequences of the inactivation of a particular factor(s) and (ii) effects resulting from the higher probability that the remaining group 2 factors associate with the RNA polymerase core.

Regulation of post-transcriptional gene expression on mRNA level in eukaryotic cells includes translocation, translation, translational repression, storage, mRNA decay, RNA silencing, and nonsense-mediated decay. These processes are associated with various RNA-binding proteins and cytoplasmic ribonucleoprotein complexes many of which are conserved across eukaryotes. Microscopically visible aggregations formed by ribonucleoprotein complexes are termed RNA granules. Stress granules where the translationally inactive mRNAs are stored and processing bodies where mRNA decay may occur present the most studied RNA granule types. Diverse RNP-granules are increasingly being assigned important roles in viral infections. Although the majority of the molecular level studies on the role of RNA granules in viral translation and replication have been conducted in mammalian systems, some studies link also plant virus infection to RNA granules. An increasing body of evidence indicates that plant viruses require components of stress granules and processing bodies for their replication and translation, but how extensively the cellular mRNA regulatory network is utilized by plant viruses has remained largely enigmatic. Antiviral RNA silencing, which is an important regulator of viral RNA stability and expression in plants, is commonly counteracted by viral suppressors of RNA silencing. Some of the RNA silencing suppressors localize to cellular RNA granules and have been proposed to carry out their suppression functions there. Moreover, plant nucleotide-binding leucine-rich repeat protein-mediated virus resistance has been linked to enhanced processing body formation and translational repression of viral RNA. Many interesting questions relate to how the pathways of antiviral RNA silencing leading to viral RNA degradation and/or repression of translation, suppression of RNA silencing and viral RNA translation converge in plants and how different RNA granules and their individual components contribute to these processes. In this review we discuss the roles of cellular RNA regulatory mechanisms and RNA granules in plant virus infection in the light of current knowledge and compare the findings to those made in animal virus studies.