Functional characterization of the role of the chromosome I partitioning system in genome segregation in Deinococcus radiodurans

Effective gene silencing using type I-E CRISPR system in the multiploid, radiation-resistant bacterium Deinococcus radiodurans

The extremely radiation-resistant bacterium, Deinococcus radiodurans, is a microbe of importance, both, for studying stress tolerance mechanisms and as a chassis for industrial biotechnology. However, the molecular tools available for use in this organism continue to be limiting, with its multiploid genome presenting an additional challenge. In view of this, the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas tools provide a large repertoire of applications for gene manipulation. We show the utility of the type I-E Cascade system for knocking down gene expression in this organism. A single-vector system was designed for the expression of the Cascade components as well as the crRNA. The type I-E Cascade system was better tolerated than the type II-A dCas9 system in D. radiodurans. An assayable acid phosphatase gene, phoN integrated into the genome of this organism could be knocked down to 10% of its activity using the Cascade system. Cascade-based knockdown of ssb, a gene important for radiation resistance resulted in poor recovery post-irradiation. Targeting the Radiation and Desiccation Response Motif (RDRM), upstream of the ssb, prevented de-repression of its expression upon radiation exposure. In addition to this, multi-locus targeting was demonstrated on the deinococcal genome, by knocking down both phoN and ssb expression simultaneously. The programmable CRISPR interference tool developed in this study will facilitate the study of essential genes, hypothetical genes, and cis-elements involved in radiation response as well as enable metabolic engineering in this organism. Further, the tool can be extended for implementing high-throughput approaches in such studies. IMPORTANCE Deinococcus radiodurans is a microbe that exhibits a very high degree of radiation resistance. In addition, it is also identified as an organism of industrial importance. We report the development of a gene-knockdown system in this organism by engineering a type I-E clustered regularly interspaced short palindromic repeat (CRISPR)-Cascade system. We used this system to silence an assayable acid phosphatase gene, phoN to 10% of its activity. The study further shows the application of the Cascade system to target an essential gene ssb, that caused poor recovery from radiation. We demonstrate the utility of CRISPR-Cascade to study the role of a regulatory cis-element in radiation response as well as for multi-gene silencing. This easy-to-implement CRISPR interference system would provide an effective tool for better understanding of complex phenomena such as radiation response in D. radiodurans and may also enhance the potential of this microbe for industrial application.

DivIVA Phosphorylation Affects Its Dynamics and Cell Cycle in Radioresistant Deinococcus radiodurans

DivIVA is a member of the Min family of proteins that spatially regulates septum formation at the midcell position and cell pole determination in Bacillus subtilis. Deinococcus radiodurans, a Gram-positive coccus-shaped bacterium, is characterized by its extreme resistance to DNA-damaging agents, including radiation. D. radiodurans cells exposed to gamma radiation undergo cell division arrest by as-yet-uncharacterized mechanisms. divIVA is shown to be an essential cell division gene in this bacterium, and DivIVA of D. radiodurans (drDivIVA) interacts with genome segregation proteins through its N-terminal region. Earlier, RqkA, a gamma radiation-responsive Ser/Thr quinoprotein kinase, was characterized for its role in radioresistance in D. radiodurans. Here, we showed that RqkA phosphorylates drDivIVA at the threonine 19 (T19) residue. The phospho-mimetic mutant with a mutation of T19 to E19 in DivIVA (DivIVAT19E) is found to be functionally different from the phospho-ablative mutant (DivIVAT19A) or the wild-type drDivIVA. A DivIVAT19E-red fluorescent protein (RFP) fusion expressed in the wild-type background showed the arrest in the typical dynamics of drDivIVA and the loss of its interaction with the genome segregation protein ParA2. The allelic replacement of divIVA with divIVAT19E-rfp was not tolerated unless drDivIVA was expressed episomally, while there was no phenotypic change when the wild-type allele was replaced with either divIVAT19A-rfp or divIVA-rfp. These results suggested that the phosphorylation of T19 in drDivIVA by RqkA affected its in vivo functions, which may contribute to the cell cycle arrest in this bacterium. IMPORTANCE Deinococcus radiodurans, a radioresistant bacterium, lacks LexA/RecA-mediated DNA damage response and cell cycle regulation as known in other bacteria. However, it adjusts its transcriptome and proteome upon DNA damage. In eukaryotes, the DNA damage response and cell cycle are regulated by Ser/Thr protein kinases. In D. radiodurans, we characterized a gamma radiation-responsive Ser/Thr quinoprotein kinase (RqkA) that phosphorylated DNA repair and cell division proteins in this bacterium. In previous work, the effect of S/T phosphorylation by RqkA on activity improvement of the DNA repair proteins has been demonstrated. This study reports that Ser phosphorylation by RqkA attenuates the function of a cell polarity and plane of cell division-determining protein, DivIVA, and its cellular dynamics in response to DNA damage, which might help to understand the mechanism of cell cycle regulation in this bacterium.

FtsZ phosphorylation brings about growth arrest upon DNA damage in Deinococcus radiodurans

The polymerization/depolymerization dynamics of FtsZ play a pivotal role in cell division in the majority of the bacteria. Deinococcus radiodurans, a radiation-resistant bacterium, shows an arrest of growth in response to DNA damage with no change in the level of FtsZ. This bacterium does not deploy LexA/RecA type of DNA damage response and cell cycle regulation, and its genome does not encode SulA homologues of Escherichia coli, which attenuate FtsZ functions in response to DNA damage in other bacteria. A radiation-responsive Ser/Thr quinoprotein kinase (RqkA), characterized for its role in radiation resistance in this bacterium, could phosphorylate several cognate proteins, including FtsZ (drFtsZ) at Serine 235 (S235) and Serine 335 (S335) residues. Here, we reported the detailed characterization of S235 and S335 phosphorylation effects in the regulation of drFtsZ functions and demonstrated that the phospho-mimetic replacements of these residues in drFtsZ had grossly affected its functions that could result in cell cycle arrest in response to DNA damage in D. radiodurans. Interestingly, the phospho-ablative replacements were found to be nearly similar to drFtsZ, whereas the phospho-mimetic mutant lost the wild-type protein's signature characteristics, including its dynamics under normal conditions. The kinetics of post-bleaching recovery for drFtsZ and phospho-mimetic mutant were nearly similar at 2 h post-irradiation recovery but were found to be different under normal conditions. These results highlighted the role of S/T phosphorylation in the regulation of drFtsZ functions and cell cycle arrest in response to DNA damage, which is demonstrated for the first time, in any bacteria.

FtsK, a DNA Motor Protein, Coordinates the Genome Segregation and Early Cell Division Processes in Deinococcus radiodurans

Filament temperature-sensitive mutant K (FtsK)/SpoIIIE family proteins are DNA translocases known as the fastest DNA motor proteins that use ATP for their movement on DNA. Most of the studies in single chromosome-containing bacteria have established the role of FtsK in chromosome dimer resolution (CDR), connecting the bacterial chromosome segregation process with cell division. Only limited reports, however, are available on the interdependent regulation of genome segregation and cell division in multipartite genome harboring (MGH) bacteria. In this study, for the first time, we report the characterization of FtsK from the radioresistant MGH bacterium Deinococcus radiodurans R1 (drFtsK). drFtsK shows the activity characteristics of a typical FtsK/SpoIIIE/Tra family. It stimulates the site-specific recombination catalyzed by Escherichia coli tyrosine recombinases. drFtsK interacts with various cell division and genome segregation proteins of D. radiodurans. Microscopic examination of different domain deletion mutants of this protein reveals alterations in cellular membrane architecture and nucleoid morphology. In vivo localization studies of drFtsK-RFP show that it forms multiple foci on nucleoid as well as on the membrane with maximum density on the septum. drFtsK coordinates its movement with nucleoid separation. The alignment of its foci shifts from old to new septum indicating its cellular dynamics with the FtsZ ring during the cell division process. Nearly, similar positional dynamicity of FtsK was observed in cells recovering from gamma radiation exposure. These results suggest that FtsK forms a part of chromosome segregation, cell envelope, and cell division machinery in D. radiodurans. IMPORTANCE Deinococcus radiodurans show extraordinary resistance to gamma radiation. It is polyploid and harbors a multipartite genome comprised of 2 chromosomes and 2 plasmids, packaged in a doughnut-shaped toroidal nucleoid. Very little is known about how the tightly packed genome is accurately segregated and the next divisional plane is determined. Filament temperature-sensitive mutant K (FtsK), a multifunctional protein, helps in pumping the septum-trapped DNA in several bacteria. Here, we characterized FtsK of D. radiodurans R1 (drFtsK) for the first time and showed it to be an active protein. The absence of drFtsK causes many defects in morphology at both cellular and nucleoid levels. The compact packaging of the deinococcal genome and cell membrane formation is hindered in ftsK mutants. In vivo drFtsK is dynamic, forms foci on both nucleoid and septum, and coordinates with FtsZ for the next cell division. Thus, drFtsK role in maintaining the normal genome phenotype and cell division in D. radiodurans is suggested.

Pan-Genome-Wide Analysis of Pantoea ananatis Identified Genes Linked to Pathogenicity in Onion

Pantoea ananatis, a gram negative and facultative anaerobic bacterium is a member of a Pantoea spp. complex that causes center rot of onion, which significantly affects onion yield and quality. This pathogen does not have typical virulence factors like type II or type III secretion systems but appears to require a biosynthetic gene-cluster, HiVir/PASVIL (located chromosomally comprised of 14 genes), for a phosphonate secondary metabolite, and the 'alt' gene cluster (located in plasmid and comprised of 11 genes) that aids in bacterial colonization in onion bulbs by imparting tolerance to thiosulfinates. We conducted a deep pan-genome-wide association study (pan-GWAS) to predict additional genes associated with pathogenicity in P. ananatis using a panel of diverse strains (n = 81). We utilized a red-onion scale necrosis assay as an indicator of pathogenicity. Based on this assay, we differentiated pathogenic (n = 51)- vs. non-pathogenic (n = 30)-strains phenotypically. Pan-genome analysis revealed a large core genome of 3,153 genes and a flexible accessory genome. Pan-GWAS using the presence and absence variants (PAVs) predicted 42 genes, including 14 from the previously identified HiVir/PASVIL cluster associated with pathogenicity, and 28 novel genes that were not previously associated with pathogenicity in onion. Of the 28 novel genes identified, eight have annotated functions of site-specific tyrosine kinase, N-acetylmuramoyl-L-alanine amidase, conjugal transfer, and HTH-type transcriptional regulator. The remaining 20 genes are currently hypothetical. Further, a core-genome SNPs-based phylogeny and horizontal gene transfer (HGT) studies were also conducted to assess the extent of lateral gene transfer among diverse P. ananatis strains. Phylogenetic analysis based on PAVs and whole genome multi locus sequence typing (wgMLST) rather than core-genome SNPs distinguished red-scale necrosis inducing (pathogenic) strains from non-scale necrosis inducing (non-pathogenic) strains of P. ananatis. A total of 1182 HGT events including the HiVir/PASVIL and alt cluster genes were identified. These events could be regarded as a major contributing factor to the diversification, niche-adaptation and potential acquisition of pathogenicity/virulence genes in P. ananatis.

DivIVA Regulates Its Expression and the Orientation of New Septum Growth in Deinococcus radiodurans

In rod-shaped Gram-negative bacteria, FtsZ localization at midcell position is regulated by the gradient of MinCDE complex across the poles. In round-shaped bacteria, which lack predefined poles, the next plane of cell division is perpendicular to the previous plane, and determination of the FtsZ assembly site is still intriguing. Deinococcus radiodurans, a coccus bacterium, is characterized by its extraordinary resistance to DNA damage. DivIVA, a putative component of the Min system in this bacterium, interacts with cognate cell division and genome segregation proteins. Here, we report that deletion of a chromosomal copy of DivIVA was possible only when the wild-type copy of DivIVA was expressed in trans on a plasmid. However, deletion of the C-terminal domain (CTD) of DivIVA (CTD mutant) was possible but produced distinguishable phenotypes, like smaller cells, slower growth, and tilted septum orientation, in D. radiodurans. In trans expression of DivIVA in the CTD mutant could restore these features of the wild type. Interestingly, the overexpression of DivIVA led to delayed separation of tetrads from an octet state in both trans-complemented divIVA-mutant and wild-type cells. The CTD mutant showed upregulation of the yggS-divIVAN operon. Both the wild type and CTD mutant formed FtsZ foci; however, unlike wild type, the position of foci in the mutant cells was found to be away from conjectural midcell position in cocci. Notably, DivIVA-red fluorescent protein (DivIVA-RFP) localizes to the septum during cell division at the new division site. These results suggested that DivIVA is an essential protein in D. radiodurans, and its C-terminal domain plays an important role in the regulation of its expression and orientation of new septal growth in this bacterium. IMPORTANCE In rod-shaped Gram-negative bacteria, the midcell position for binary fission is relatively easy to model. In cocci that do not have predefined poles, the plane of next cell division is shown to be perpendicular to the previous plane. However, the molecular basis of perpendicularity is not known in cocci. The DivIVA protein of Deinococcus radiodurans, a coccus bacterium, physically interacts with the septum and establishes macromolecular interactions with genome segregation proteins through its N-terminal domain and with MinC through the C-terminal domain. Here, we have brought forth some evidence to suggest that DivIVA is essential for growth and plays an important role in cell polarity determination, and its C-terminal domain plays a crucial role in the growth of new septa in the correct orientation as well as in the regulation of DivIVA expression.

Molecular interactions and their predictive roles in cell pole determination in bacteria

Bacterial cell cycle is divided into well-coordinated phases; chromosome duplication and segregation, cell elongation, septum formation, and cytokinesis. The temporal separation of these phases depends upon the growth rates and doubling time in different bacteria. The entire process of cell division starts with the assembly of divisome complex at mid-cell position followed by constriction of the cell wall and septum formation. In the mapping of mid-cell position for septum formation, the gradient of oscillating Min proteins across the poles plays a pivotal role in several bacteria genus. The cues in the cell that defines the poles and plane of cell division are not fully characterized in cocci. Recent studies have shed some lights on molecular interactions at the poles and the underlying mechanisms involved in pole determination in non-cocci. In this review, we have brought forth recent findings on these aspects together, which would suggest a model to explain the mechanisms of pole determination in rod shaped bacteria and could be extrapolated as a working model in cocci.

Characterization of ori and parS-like functions in secondary genome replicons in Deinococcus radiodurans

The mechanisms underlying multipartite genome maintenance and its functional significance in extraordinary radioresistance of Deinococcus radiodurans are not well understood. The sequences upstream to parAB operons in chrII (cisII) and MP (cisMP) could stabilize an otherwise, non-replicative colE1 plasmid, in D. radiodurans DnaA and cognate ParB proteins bound specifically with cisII and cisMP elements. The ΔcisII and ΔcisMP cells showed the reduced copy number of cognate replicons and radioresistance as compared with wild type. Fluorescent reporter-operator system inserted in chrI, chrII, and MP in wild type and cisII mutants showed the presence of all three replicons in wild-type cells. Although chrI was present in all the ΔcisII and ΔcisMP cells, nearly half of these cells had chrII and MP, respectively, and the other half had the reduced number of foci representing these replications. These results suggested that cisII and cisMP elements contain both origin of replication and parS-like functions and the secondary genome replicons (chrII and MP) are maintained independent of chrI and have roles in radioresistance of D. radiodurans.

Comparative genomics of wild-type and laboratory-evolved biofilm-overproducing Deinococcus metallilatus strains

Deinococcus metallilatus MA1002 was exposed to ultraviolet radiation to generate mutants with enhanced biofilm production. Two strains (nos 5 and 6) were then selected based on their high biofilm formation, as well as their possession of higher concentrations of extracellular matrix components (eDNA, protein and saccharides) than the wild-type (WT). Genomic sequencing revealed the presence of large genome deletions in a secondary chromosome in the mutants. Expression analyses of the WT and mutant strains indicated the upregulation of genes associated with exopolysaccharide synthesis and stress response. The mutant strains showed high mortality in glucose-supplemented (TYG) medium; however, cell death and biofilm formation were not increased in mutant cells grown under acetate- or glyoxylate-added media, suggesting that metabolic toxicity during glucose metabolism induced a high rate of cell death but improved biofilm formation in mutant strains. In damaged cells, eDNAs contributed to the enhanced biofilm formation of D. metallilatus.

Bacterial chromosome segregation by the ParABS system

Proper chromosome segregation during cell division is essential in all domains of life. In the majority of bacterial species, faithful chromosome segregation is mediated by the tripartite ParABS system, consisting of an ATPase protein ParA, a CTPase and DNA-binding protein ParB, and a centromere-like parS site. The parS site is most often located near the origin of replication and is segregated first after chromosome replication. ParB nucleates on parS before binding to adjacent non-specific DNA to form a multimeric nucleoprotein complex. ParA interacts with ParB to drive the higher-order ParB–DNA complex, and hence the replicating chromosomes, to each daughter cell. Here, we review the various models for the formation of the ParABS complex and describe its role in segregating the origin-proximal region of the chromosome. Additionally, we discuss outstanding questions and challenges in understanding bacterial chromosome segregation.

Chromosome Segregation Proteins as Coordinators of Cell Cycle in Response to Environmental Conditions

Chromosome segregation is a crucial stage of the cell cycle. In general, proteins involved in this process are DNA-binding proteins, and in most bacteria, ParA and ParB are the main players; however, some bacteria manage this process by employing other proteins, such as condensins. The dynamic interaction between ParA and ParB drives movement and exerts positioning of the chromosomal origin of replication (oriC) within the cell. In addition, both ParA and ParB were shown to interact with the other proteins, including those involved in cell division or cell elongation. The significance of these interactions for the progression of the cell cycle is currently under investigation. Remarkably, DNA binding by ParA and ParB as well as their interactions with protein partners conceivably may be modulated by intra- and extracellular conditions. This notion provokes the question of whether chromosome segregation can be regarded as a regulatory stage of the cell cycle. To address this question, we discuss how environmental conditions affect chromosome segregation and how segregation proteins influence other cell cycle processes.

Rules and Exceptions: The Role of Chromosomal ParB in DNA Segregation and Other Cellular Processes

The segregation of newly replicated chromosomes in bacterial cells is a highly coordinated spatiotemporal process. In the majority of bacterial species, a tripartite ParAB-parS system, composed of an ATPase (ParA), a DNA-binding protein (ParB), and its target(s) parS sequence(s), facilitates the initial steps of chromosome partitioning. ParB nucleates around parS(s) located in the vicinity of newly replicated oriCs to form large nucleoprotein complexes, which are subsequently relocated by ParA to distal cellular compartments. In this review, we describe the role of ParB in various processes within bacterial cells, pointing out interspecies differences. We outline recent progress in understanding the ParB nucleoprotein complex formation and its role in DNA segregation, including ori positioning and anchoring, DNA condensation, and loading of the structural maintenance of chromosome (SMC) proteins. The auxiliary roles of ParBs in the control of chromosome replication initiation and cell division, as well as the regulation of gene expression, are discussed. Moreover, we catalog ParB interacting proteins. Overall, this work highlights how different bacterial species adapt the DNA partitioning ParAB-parS system to meet their specific requirements.

ParA proteins of secondary genome elements cross-talk and regulate radioresistance through genome copy number reduction in Deinococcus radiodurans

Deinococcus radiodurans, an extremely radioresistant bacterium has a multipartite genome system and ploidy. Mechanisms underlying such types of bacterial genome maintenance and its role in extraordinary radioresistance are not known in this bacterium. Chromosome I (Chr I), chromosome II (Chr II) and megaplasmid (Mp) encode its own set of genome partitioning proteins. Here, we have characterized P-loop ATPases of Chr II (ParA2) and Mp (ParA3) and their roles in the maintenance of genome copies and extraordinary radioresistance. Purified ParA2 and ParA3 showed nearly similar polymerization kinetics and interaction patterns with DNA. Electron microscopic examination of purified proteins incubated with DNA showed polymerization on nicked circular dsDNA. ParA2 and ParA3 showed both homotypic and heterotypic interactions to each other, but not with ParA1 (ParA of Chr I). Similarly, ParA2 and ParA3 interacted with ParB2 and ParB3 but not with ParB1 in vivo. ParB2 and ParB3 interaction with cis-elements located upstream to the corresponding parAB operon was found to be sequence-specific. Unlike single mutant of parA2 and parA3, their double mutant (ΔparA2ΔParA3) affected copy number of cognate genome elements and resistance to γ-radiation as well as hydrogen peroxide in this bacterium. These results suggested that ParA2 and ParA3 are DNA-binding ATPases producing higher order polymers on DNA and are functionally redundant in the maintenance of secondary genome elements in D. radiodurans. The findings also suggest the involvement of secondary genome elements such as Chr II and Mp in the extraordinary radioresistance of D. radiodurans.

Plasmids for making multiple knockouts in a radioresistant bacterium Deinococcus radiodurans

The gene knockouts are mostly created using homologous recombination-based replacement of target gene(s) with the expressing cassette of selection marker gene(s). Here, we constructed a series of plasmids bearing the expressing cassettes of genes encoding different antibiotics markers like nptII (Kan^R), aadA (Spec^R), cat (Cm^R) and aac(3) (Gen^R). D. radiodurans is a radioresistant Gram positive bacterium that does not support the independent maintenance of colE1 origin-based plasmids. Using these constructs, the disruption mutants of both single and multiple genes involved in segregation of secondary genome elements have been generated in this bacterium. Unlike single mutants, the double and triple mutants showed growth retardation under normal growth conditions and the synergistic effects with Topoisomerase II inhibitor on the growth of this bacterium. Thus, these plasmids could be useful in creating multiple deletions/disruptions in bacteria that do not support independent maintenance of colE1 origin-based plasmid.

Maintenance of multipartite genome system and its functional significance in bacteria

Bacteria are unicellular organisms that do not show compartmentalization of the genetic material and other cellular organelles as seen in higher organisms. Earlier, bacterial genomes were defined as single circular chromosome and extrachromosomal plasmids. Recently, many bacteria were found harbouringmultipartite genome system and the numbers of copies of genome elements including chromosomes vary from one to several per cell. Interestingly, it is noticed that majority of multipartite genome-harbouring bacteria are either stress tolerant or pathogens. Further, it is observed that the secondary genomes in these bacteria encode proteins that are involved in bacterial genome maintenance and also contribute to higher stress tolerance, and pathogenicity in pathogenic bacteria. Surprisingly, in some bacteria the genes encoding the proteins of classical homologous recombination pathways are present only on the secondary chromosomes, and some do not have either of the classical homologous recombination pathways. This review highlights the presence of ploidy and multipartite genomes in bacterial system, the underlying mechanisms of genome maintenance and the possibilities of these features contributing to higher abiotic and biotic stress tolerance in these bacteria.

Phosphorylation of FtsZ and FtsA by a DNA Damage-Responsive Ser/Thr Protein Kinase Affects Their Functional Interactions in Deinococcus radiodurans

The LexA/RecA-type SOS response is the only characterized mechanism of DNA damage response in bacteria. It regulates cell cycle by attenuating the functions of cell division protein FtsZ and inducing the expression of DNA repair proteins. There are bacteria, including Deinococcus radiodurans, that do not show this classical SOS response. D. radiodurans is known for its extraordinary resistance to gamma radiation, and a DNA damage-responsive Ser/Thr protein kinase (RqkA) has been characterized for its role in radioresistance. RqkA phosphorylates a large number of proteins in solution. The phosphorylation of RecA and PprA by RqkA enhanced their activities. FtsZ phosphorylation is inducible by gamma radiation in wild-type D. radiodurans but not in an rqkA mutant. Phosphorylation affected the interaction of FtsZ and FtsA in this bacterium. This study, therefore, brought forth some findings that might lead to the discovery of a new mechanism regulating the bacterial cell cycle in response to DNA damage.

Deinococcus radiodurans, a highly radioresistant bacterium, does not show LexA-dependent regulation of recA expression in response to DNA damage. On the other hand, phosphorylation of DNA repair proteins such as PprA and RecA by a DNA damage-responsive Ser/Thr protein kinase (STPK) (RqkA) could improve their DNA metabolic activities as well as their roles in the radioresistance of D. radiodurans. Here we report RqkA-mediated phosphorylation of cell division proteins FtsZ and FtsA in vitro and in surrogate Escherichia coli bacteria expressing RqkA. Mass spectrometric analysis mapped serine 235 and serine 335 in FtsZ and threonine 272, serine 370, and serine 386 in FtsA as potential phosphorylation sites. Although the levels of FtsZ did not change during postirradiation recovery (PIR), phosphorylation of both FtsZ and FtsA showed a kinetic change during PIR. However, in an rqkA mutant of D. radiodurans, though FtsZ underwent phosphorylation, no kinetic change in phosphorylation was observed. Further, RqkA adversely affected FtsA interaction with FtsZ, and phosphorylated FtsZ showed higher GTPase activity than unphosphorylated FtsZ. These results suggest that both FtsZ and FtsA are phosphoproteins in D. radiodurans. The increased phosphorylation of FtsZ in response to radiation damage in the wild-type strain but not in an rqkA mutant seems to be regulating the functional interaction of FtsZ with FtsA. For the first time, we demonstrate the role of a DNA damage-responsive STPK (RqkA) in the regulation of functional interaction of cell division proteins in this bacterium.

IMPORTANCE The LexA/RecA-type SOS response is the only characterized mechanism of DNA damage response in bacteria. It regulates cell cycle by attenuating the functions of cell division protein FtsZ and inducing the expression of DNA repair proteins. There are bacteria, including Deinococcus radiodurans, that do not show this classical SOS response. D. radiodurans is known for its extraordinary resistance to gamma radiation, and a DNA damage-responsive Ser/Thr protein kinase (RqkA) has been characterized for its role in radioresistance. RqkA phosphorylates a large number of proteins in solution. The phosphorylation of RecA and PprA by RqkA enhanced their activities. FtsZ phosphorylation is inducible by gamma radiation in wild-type D. radiodurans but not in an rqkA mutant. Phosphorylation affected the interaction of FtsZ and FtsA in this bacterium. This study, therefore, brought forth some findings that might lead to the discovery of a new mechanism regulating the bacterial cell cycle in response to DNA damage.

DdrI, a cAMP Receptor Protein Family Member, Acts as a Major Regulator for Adaptation of Deinococcus radiodurans to Various Stresses

The DNA damage response ddrI gene encodes a transcription regulator belonging to the cAMP receptor protein (CRP) family. Cells devoid of the DdrI protein exhibit a pleiotropic phenotype, including growth defects and sensitivity to DNA-damaging agents and to oxidative stress. Here, we show that the absence of the DdrI protein also confers sensitivity to heat shock treatment, and several genes involved in heat shock response were shown to be upregulated in a DdrI-dependent manner. Interestingly, expression of the Escherichia coli CRP partially compensates for the absence of the DdrI protein. Microscopic observations of ΔddrI mutant cells revealed an increased proportion of two-tetrad and anucleated cells in the population compared to the wild-type strain, indicating that DdrI is crucial for the completion of cell division and/or chromosome segregation. We show that DdrI is also involved in the megaplasmid MP1 stability and in efficient plasmid transformation by facilitating the maintenance of the incoming plasmid in the cell. The in silico prediction of putative DdrI binding sites in the D. radiodurans genome suggests that hundreds of genes, belonging to several functional groups, may be regulated by DdrI. In addition, the DdrI protein absolutely requires cAMP for in vitro binding to specific target sequences, and it acts as a dimer. All these data underline the major role of DdrI in D. radiodurans physiology under normal and stress conditions by regulating, both directly and indirectly, a cohort of genes involved in various cellular processes, including central metabolism and specific responses to diverse harmful environments.IMPORTANCEDeinococcus radiodurans has been extensively studied to elucidate the molecular mechanisms responsible for its exceptional ability to withstand lethal effects of various DNA-damaging agents. A complex network, including efficient DNA repair, protein protection against oxidation, and diverse metabolic pathways, plays a crucial role for its radioresistance. The regulatory networks orchestrating these various pathways are still missing. Our data provide new insights into the crucial contribution of the transcription factor DdrI for the D. radiodurans ability to withstand harmful conditions, including UV radiation, mitomycin C treatment, heat shock, and oxidative stress. Finally, we highlight that DdrI is also required for accurate cell division, for maintenance of plasmid replicons, and for central metabolism processes responsible for the overall cell physiology.

drFrnE Represents a Hitherto Unknown Class of Eubacterial Cytoplasmic Disulfide Oxido-Reductases

AIMS

Living cells employ thioredoxin and glutaredoxin disulfide oxido-reductases to protect thiol groups in intracellular proteins. FrnE protein of Deinococcus radiodurans (drFrnE) is a disulfide oxido-reductase that is induced in response to Cd²⁺ exposure and is involved in cadmium and radiation tolerance. The aim of this study is to probe structure, function, and cellular localization of FrnE class of proteins.

RESULTS

Here, we show drFrnE as a novel cytoplasmic oxido-reductase that could be functional in eubacteria under conditions where thioredoxin/glutaredoxin systems are inhibited or absent. Crystal structure analysis of drFrnE reveals thioredoxin fold with an alpha helical insertion domain and a unique, flexible, and functionally important C-terminal tail. The C-tail harbors a novel 239-CX₄C-244 motif that interacts with the active site 22-CXXC-25 motif. Crystal structures with different active site redox states, including mixed disulfide (Cys22-Cys244), are reported here. The biochemical data show that 239-CX₄C-244 motif channels electrons to the active site cysteines. drFrnE is more stable in the oxidized form, compared with the reduced form, supporting its role as a disulfide reductase. Using bioinformatics analysis and fluorescence microscopy, we show cytoplasmic localization of drFrnE. We have found "true" orthologs of drFrnE in several eubacterial phyla and, interestingly, all these groups apparently lack a functional glutaredoxin system. Innovation and Conclusion: We show that drFrnE represents a new class of hitherto unknown intracellular oxido-reductases that are abundantly present in eubacteria. Unlike other well-known oxido-reductases, FrnE harbors an additional dithiol motif that acts as a conduit to channel electrons to the active site during catalytic turnover. Antioxid. Redox Signal. 28, 296-310.

Novel Chromosome Organization Pattern in Actinomycetales-Overlapping Replication Cycles Combined with Diploidy

Bacteria regulate chromosome replication and segregation tightly with cell division to ensure faithful segregation of DNA to daughter generations. The underlying mechanisms have been addressed in several model species. It became apparent that bacteria have evolved quite different strategies to regulate DNA segregation and chromosomal organization. We have investigated here how the actinobacterium Corynebacterium glutamicum organizes chromosome segregation and DNA replication. Unexpectedly, we found that C. glutamicum cells are at least diploid under all of the conditions tested and that these organisms have overlapping C periods during replication, with both origins initiating replication simultaneously. On the basis of experimental data, we propose growth rate-dependent cell cycle models for C. glutamicum.

Bacterial cell cycles are known for few model organisms and can vary significantly between species. Here, we studied the cell cycle of Corynebacterium glutamicum, an emerging cell biological model organism for mycolic acid-containing bacteria, including mycobacteria. Our data suggest that C. glutamicum carries two pole-attached chromosomes that replicate with overlapping C periods, thus initiating a new round of DNA replication before the previous one is terminated. The newly replicated origins segregate to midcell positions, where cell division occurs between the two new origins. Even after long starvation or under extremely slow-growth conditions, C. glutamicum cells are at least diploid, likely as an adaptation to environmental stress that may cause DNA damage. The cell cycle of C. glutamicum combines features of slow-growing organisms, such as polar origin localization, and fast-growing organisms, such as overlapping C periods.

Phosphorylation of Deinococcus radiodurans RecA Regulates Its Activity and May Contribute to Radioresistance

Deinococcus radiodurans has a remarkable capacity to survive exposure to extreme levels of radiation that cause hundreds of DNA double strand breaks (DSBs). DSB repair in this bacterium depends on its recombinase A protein (DrRecA). DrRecA plays a pivotal role in both extended synthesis-dependent strand annealing and slow crossover events of DSB repair during the organism's recovery from DNA damage. The mechanisms that control DrRecA activity during the D. radiodurans response to γ radiation exposure are unknown. Here, we show that DrRecA undergoes phosphorylation at Tyr-77 and Thr-318 by a DNA damage-responsive serine threonine/tyrosine protein kinase (RqkA). Phosphorylation modifies the activity of DrRecA in several ways, including increasing its affinity for dsDNA and its preference for dATP over ATP. Strand exchange reactions catalyzed by phosphorylated versus unphosphorylated DrRecA also differ. In silico analysis of DrRecA structure support the idea that phosphorylation can modulate crucial functions of this protein. Collectively, our findings suggest that phosphorylation of DrRecA enables the recombinase to selectively use abundant dsDNA substrate present during post-irradiation recovery for efficient DSB repair, thereby promoting the extraordinary radioresistance of D. radiodurans.

PprA, a pleiotropic protein for radioresistance, works through DNA gyrase and shows cellular dynamics during postirradiation recovery in Deinococcus radiodurans

PprA, a pleiotropic protein involved in radioresistance of Deinococcus radiodurans was detected in multiprotein DNA processing complex identified from this bacterium. pprA mutant expressing GFP-PprA could restore its wild type resistance of γ radiation. Under normal conditions, GFP-PprA expressing cells showed PprA localization on both septum trapped nucleoids (STN) and nucleoids located elsewhere (MCN). Cell exposed to 4 kGy γ radiation showed nearly 2 h growth lag and during this growth arrest phase, the majority of the cells had GFP-PprA located on MCN. While in late phase (~120 min) PIR cells, when cells are nearly out of growth arrest, PprA was maximally found with STN. These cells when treated with nalidixic acid showed diffused localization of PprA across the septum. gyrA disruption mutant of D. radiodurans showed growth inhibition, which increased further in gyrA pprA mutant. Interestingly, gyrA mutant showed ~20-fold less resistance to γ radiation as compared to wild type, which did increase further in gyrA pprA mutant. These results suggested that PprA localization undergoes a dynamic change during PIR, and its localization on nucleoid near septum and functional interaction with gyrase A might suggest a mechanism that could explain PprA role in genome segregation possibly through topoisomerase II.

Dr-FtsA, an actin homologue in Deinococcus radiodurans differentially affects Dr-FtsZ and Ec-FtsZ functions in vitro

The Deinococcus radiodurans genome encodes homologues of divisome proteins including FtsZ and FtsA. FtsZ of this bacterium (Dr-FtsZ) has been recently characterized. In this paper, we study FtsA of D. radiodurans (Dr-FtsA) and its involvement in regulation of FtsZ function. Recombinant Dr-FtsA showed neither ATPase nor GTPase activity and its polymerization was ATP dependent. Interestingly, we observed that Dr-FtsA, when compared with E. coli FtsA (Ec-FtsA), has lower affinity for both Dr-FtsZ and Ec-FtsZ. Also, Dr-FtsA showed differential effects on GTPase activity and sedimentation characteristics of Dr-FtsZ and Ec-FtsZ. For instance, Dr-FtsA stimulated GTPase activity of Dr-FtsZ while GTPase activity of Ec-FtsZ was reduced in the presence of Dr-FtsA. Stimulation of GTPase activity of Dr-FtsZ by Dr-FtsA resulted in depolymerization of Dr-FtsZ. Dr-FtsA effects on GTPase activity and polymerization/depolymerisation characteristics of Dr-FtsZ did not change significantly in the presence of ATP. Recombinant E. coli expressing Dr-FtsA showed cell division inhibition in spite of in trans expression of Dr-FtsZ in these cells. These results suggested that Dr-FtsA, although it lacks ATPase activity, is still functional and differentially affects Dr-FtsZ and Ec-FtsZ function in vitro.

FtsZDr, a tubulin homologue in radioresistant bacterium Deinococcus radiodurans is characterized as a GTPase exhibiting polymerization/depolymerization dynamics in vitro and FtsZ ring formation in vivo

The GTPase-dependent polymerization/depolymerization dynamics of FtsZ regulate bacterial cell division in vivo. Deinococcus radiodurans is better known for its extraordinary radioresistance and therefore, the characterization of FtsZ of this bacterium (FtsZDr) would be required to understand the mechanisms underlying regulation of cell division in response to DNA damage. Recombinant FtsZDr bound to GTP and showed GTPase activity. It produced bundles of protofilaments in the presence of either GTP or Mg2+ ions. But the formation of the higher size ordered structures required both GTP and Mg2+ in vitro. It showed polymerization/depolymerization dynamics as a function of GTP and Mg2+. Interestingly, ATP interacted with FtsZDr and stimulated its GTPase activity by ∼2-fold possibly by increasing both substrate affinity and rate of reaction. FtsZDr-GFP expressing in D. radiodurans produced typical Z ring perpendicular to the plane of first cell division. These results suggested that FtsZDr is a GTPase in vitro and produces typical Z ring at the mid cell position in D. radiodurans.

ParABS system in chromosome partitioning in the bacterium Myxococcus xanthus

Chromosome segregation is an essential cellular function in eukaryotic and prokaryotic cells. The ParABS system is a fundamental player for a mitosis-like process in chromosome partitioning in many bacterial species. This work shows that the social bacterium Myxococcus xanthus also uses the ParABS system for chromosome segregation. Its large prokaryotic genome of 9.1 Mb contains 22 parS sequences near the origin of replication, and it is shown here that M. xanthus ParB binds preferentially to a consensus parS sequence in vitro. ParB and ParA are essential for cell viability in M. xanthus as in Caulobacter crescentus, but unlike in many other bacteria. Absence of ParB results in anucleate cells, chromosome segregation defects and loss of viability. Analysis of ParA subcellular localization shows that it clusters at the poles in all cells, and in some, in the DNA-free cell division plane between two chromosomal DNA masses. This ParA localization pattern depends on ParB but not on FtsZ. ParB inhibits the nonspecific interaction of ParA with DNA, and ParA colocalizes with chromosomal DNA only when ParB is depleted. The subcellular localization of ParB suggests a single ParB-parS complex localized at the edge of the nucleoid, next to a polar ParA cluster, with a second ParB-parS complex migrating after the replication of parS takes place to the opposite nucleoid edge, next to the other polar ParA cluster.

PprA contributes to Deinococcus radiodurans resistance to nalidixic acid, genome maintenance after DNA damage and interacts with deinococcal topoisomerases

PprA is known to contribute to Deinococcus radiodurans' remarkable capacity to survive a variety of genotoxic assaults. The molecular bases for PprA's role(s) in the maintenance of the damaged D. radiodurans genome are incompletely understood, but PprA is thought to promote D. radiodurans's capacity for DSB repair. PprA is found in a multiprotein DNA processing complex along with an ATP type DNA ligase, and the D. radiodurans toposiomerase IB (DraTopoIB) as well as other proteins. Here, we show that PprA is a key contributor to D. radiodurans resistance to nalidixic acid (Nal), an inhibitor of topoisomerase II. Growth of wild type D. radiodurans and a pprA mutant were similar in the absence of exogenous genotoxic insults; however, the pprA mutant exhibited marked growth delay and a higher frequency of anucleate cells following treatment with DNA-damaging agents. We show that PprA interacts with both DraTopoIB and the Gyrase A subunit (DraGyrA) in vivo and that purified PprA enhances DraTopoIB catalysed relaxation of supercoiled DNA. Thus, besides promoting DNA repair, our findings suggest that PprA also contributes to preserving the integrity of the D. radiodurans genome following DNA damage by interacting with DNA topoisomerases and by facilitating the actions of DraTopoIB.

Tracking of chromosome and replisome dynamics in Myxococcus xanthus reveals a novel chromosome arrangement

Cells closely coordinate cell division with chromosome replication and segregation; however, the mechanisms responsible for this coordination still remain largely unknown. Here, we analyzed the spatial arrangement and temporal dynamics of the 9.1 Mb circular chromosome in the rod-shaped cells of Myxococcus xanthus. For chromosome segregation, M. xanthus uses a parABS system, which is essential, and lack of ParB results in chromosome segregation defects as well as cell divisions over nucleoids and the formation of anucleate cells. From the determination of the dynamic subcellular location of six genetic loci, we conclude that in newborn cells ori, as monitored following the ParB/parS complex, and ter regions are localized in the subpolar regions of the old and new cell pole, respectively and each separated from the nearest pole by approximately 1 µm. The bulk of the chromosome is arranged between the two subpolar regions, thus leaving the two large subpolar regions devoid of DNA. Upon replication, one ori region remains in the original subpolar region while the second copy segregates unidirectionally to the opposite subpolar region followed by the rest of the chromosome. In parallel, the ter region of the mother chromosome relocates, most likely passively, to midcell, where it is replicated. Consequently, after completion of replication and segregation, the two chromosomes show an ori-ter-ter-ori arrangement with mirror symmetry about a transverse axis at midcell. Upon completion of segregation of the ParB/parS complex, ParA localizes in large patches in the DNA-free subpolar regions. Using an Ssb-YFP fusion as a proxy for replisome localization, we observed that the two replisomes track independently of each other from a subpolar region towards ter. We conclude that M. xanthus chromosome arrangement and dynamics combine features from previously described systems with new features leading to a novel spatiotemporal arrangement pattern.

Work on several model organisms has revealed that bacterial chromosomes are spatially highly arranged throughout the cell cycle in a dynamic yet reproducible manner. These analyses have also demonstrated significant differences between chromosome arrangements and dynamics in different bacterial species. Here, we show that the Myxococcus xanthus genome is arranged about a longitudinal axis with ori in a subpolar region and ter in the opposite subpolar region. Upon replication, one ori remains at the original subpolar region while the second copy in a directed and parABS-dependent manner segregates to the opposite subpolar region followed by the rest of the chromosome. In parallel, ter relocates from a subpolar region to midcell. Replication involves replisomes that track independently of each other from the ori-containing subpolar region towards ter. Moreover, we find that the parABS system is essential in M. xanthus and ParB depletion not only results in chromosome segregation defects but also in cell division defects with cell divisions occurring over nucleoids. In M. xanthus the dynamics of chromosome replication and segregation combine features from previously described systems leading to a novel spatiotemporal arrangement pattern.

Structure-function study of deinococcal serine/threonine protein kinase implicates its kinase activity and DNA repair protein phosphorylation roles in radioresistance of Deinococcus radiodurans

The DR2518 (RqkA) a eukaryotic type serine/threonine protein kinase in Deinococcus radiodurans was characterized for its role in bacterial response to oxidative stress and DNA damage. The K42A, S162A, T169A and S171A mutation in RqkA differentially affected its kinase activity and functional complementation for γ radiation resistance in Δdr2518 mutant. For example, K42A mutant was completely inactive and showed no complementation while S171A, T169A and T169A/S171A mutants were less active and complemented proportionally to different levels as compared to wild type. Amongst, different DNA binding proteins that purified RqkA could phosphorylate, PprA a DNA repair protein, phosphorylation had improved its affinity to DNA by 4 fold and could enhance its supportive role in intermolecular ligation by T4 DNA ligase. RqkA phosphorylates PprA at threonine 72 (T72), serine 112 (S112) and threonine 144 (T144) in vitro with the majority of it goes to T72 site. Unlike wild type PprA and single mutants of T72, S112 and T144 residues, the T72AS112A double and T72AS112AT144A triple mutant derivatives of PprA did not phosphorylate in vivo and also failed to complement PprA loss in D. radiodurans. Deletion of rqkA in pprA::cat background enhanced radiosensitivity of pprA mutant, which became nearly similar to ΔrqkA resistance to γ radiation. These results suggested that K42 of RqkA is essential for catalytic functions and the kinase activity of RqkA as well as phosphorylation of PprA have roles in γ radiation resistance of D. radiodurans.

DR1769, a protein with N-terminal beta propeller repeats and a low-complexity hydrophilic tail, plays a role in desiccation tolerance of Deinococcus radiodurans

The Deinococcus radiodurans genome encodes five putative quinoproteins. Among these, the Δdr2518 and Δdr1769 mutants became sensitive to gamma radiation. DR2518 with beta propeller repeats in the C-terminal domain was characterized as a radiation-responsive serine/threonine protein kinase in this bacterium. DR1769 contains beta propeller repeats at the N terminus, while its C-terminal domain is a proline-rich disordered structure and constitutes a low-complexity hydrophilic region with aliphatic-proline dipeptide motifs. The Δdr1769 mutant showed nearly a 3-log cycle sensitivity to desiccation at 5% humidity compared to that of the wild type. Interestingly, the gamma radiation and mitomycin C (MMC) resistance in mutant cells also dropped by ∼1-log cycle at 10 kGy and ∼1.5-fold, respectively, compared to those in wild-type cells. But there was no effect of UV (254 nm) exposure up to 800 J · m(-2). These cells showed defective DNA double-strand break repair, and the average size of the nucleoid in desiccated wild-type and Δdr1769 cells was reduced by approximately 2-fold compared to that of respective controls. However, the nucleoid in wild-type cells returned to a size almost similar to that of the untreated control, which did not happen in mutant cells, at least up to 24 h postdesiccation. These results suggest that DR1769 plays an important role in desiccation and radiation resistance of D. radiodurans, possibly by protecting genome integrity under extreme conditions.