ATP-dependent proteinases in bacteria

Pedobacter rhodius sp. nov. and Pedobacter punctiformis sp. nov., isolated from soil

Two Gram-staining negative, catalase- and oxidase-positive, pinkish-colored and rod-shaped strains, designated SJ11T and HCMS5-2 T, were isolated from soil in South Korea. The growth of strain SJ11T was observed from 15℃ to 35℃ (optimum, 30℃), from pH 6.0 to 11.0 (optimum, pH 6.0-7.0) and with NaCl 0-1% (w/v) (optimum, 0%) and that of strain HCMS5-2 T was observed from 4℃ to 40℃ (optimum, 25℃), from pH 6.0 to pH 8.0 (optimum, pH 7.0) and with NaCl 0-5% (w/v) (optimum, 0-1%). Phylogenetic analysis based on 16S rRNA gene sequences showed that both strains belonged to the genus Pedobacter. Strain SJ11T had the highest 16S rRNA similarities with Pedobacter jejuensis THG-DR3T (98.5%) and strain HCMS5-2 T had the highest similarities with Pedobacter nototheniae 36B243T (98.7%). The digital DNA-DNA hybridization value of strain SJ11T with Pedobacter jejuensis THG-DR3T was 23.6%, with an average nucleotide identity value of 79.6%, and that of strain HCMS5-2 T with Pedobacter nototheniae 36B243T was 26.4%, with an average nucleotide identity value of 83.1%. The predominant cellular fatty acids (> 10%) of SJ11T and HCMS5-2 T were iso-C15:0, summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c) and iso-C17:0 3-OH. The genome size of strain SJ11T was approximately 4.7 Mb with a G + C content of 37.7% and that of strain HCMS5-2 T was approximately 4.1 Mb with a G + C content of 36.4%. The major polar lipid and respiratory quinone of SJ11T and HCMS5-2 T were phosphatidylethanolamine and menaquinone NK-7, respectively. Results of this study showed that strains SJ11T and HCMS5-2 T belonged to the genus Pedobacter as novel species, of which the name Pedobacter rhodius sp. nov., with the type strain SJ11T (= KACC 22884 T = TBRC 16597 T) and Pedobacter punctiformis sp. nov., with the type strain HCMS5-2 T (= KACC 22863 T = TBRC 16598 T) were respectively proposed.

Chryseobacterium luquanense sp. nov., a casein-hydrolysing bacterium from the Jiaozi Mountain in Yunnan, PR China

Strain KC 927T was isolated during an investigation of the soil bacteria diversity on Jiaozi Mountain, central Yunnan, Southwest China. The strain was Gram-stain-negative, rod-shaped, non-motile, oxidase-negative, catalase-positive and aerobic. Results of 16S rRNA gene alignment and phylogenetic analysis indicated that strain KC 927T was a member of the genus Chryseobacterium and closely related to Chryseobacterium caseinilyticum GCR10T (98.4%), Chryseobacterium piscicola DSM 21068T (98.3 %) and 'Chryseobacterium formosus' CCTCC AB 2015118T (97.9 %). With a genome size of 4 348 708 bp, strain KC 927T had 33.5 mol% DNA G+C content and contained 4012 protein-coding genes and 77 RNA genes. The average nucleotide identity and digital DNA-DNA hybridization values between strain KC 927T and C. caseinilyticum GCR10T, C. piscicola DSM 21068T and 'C. formosus' CCTCC AB 2015118T were 80.1, 79.6 and 90.7 %, and 25.5, 23.6 and 42.0 %, respectively. The main polar lipid of strain KC 927T was phosphatidylethanolamine and the respiratory quinone was MK-6. The major fatty acids (≥10 %) were iso-C15 : 0, iso-C17 : 1  ω9c and iso-C17 : 0 3-OH. Evidence from phenotypic, phylogenetic and chemotaxonomic analyses support that strain KC 927T represents a new species of the genus Chryseobacterium, for which the name Chryseobacterium luquanense sp. nov. is proposed. The type strain is KC 927T (=CGMCC 1.18760T=JCM 35707T).

Temperature Matters: Bacterial Response to Temperature Change

Temperature is one of the most important factors in all living organisms for survival. Being a unicellular organism, bacterium requires sensitive sensing and defense mechanisms to tolerate changes in temperature. During a temperature shift, the structure and composition of various cellular molecules including nucleic acids, proteins, and membranes are affected. In addition, numerous genes are induced during heat or cold shocks to overcome the cellular stresses, which are known as heat- and cold-shock proteins. In this review, we describe the cellular phenomena that occur with temperature change and bacterial responses from a molecular perspective, mainly in Escherichia coli.

PrkA is an ATP-dependent protease that regulates sporulation in Bacillus subtilis

In Bacillus subtilis, sporulation is a sequential and highly regulated process. Phosphorylation events by histidine kinases are key points in the phosphorelay that initiates sporulation, but serine/threonine protein kinases also play important auxiliary roles in this regulation. PrkA has been proposed to be a serine protein kinase expressed during the initiation of sporulation and involved in this differentiation process. Additionally, the role of PrkA in sporulation has been previously proposed to be mediated via the transition phase regulator ScoC, which in turn regulates the transcriptional factor σ^K and its regulon. However, the kinase activity of PrkA has not been clearly demonstrated, and neither its autophosphorylation nor phosphorylated substrates have been unambiguously established in B. subtilis. We demonstrated here that PrkA regulation of ScoC is likely indirect. Following bioinformatic homology searches, we revealed sequence similarities of PrkA with the ATPases associated with diverse cellular activities ATP-dependent Lon protease family. Here, we showed that PrkA is indeed able to hydrolyze α-casein, an exogenous substrate of Lon proteases, in an ATP-dependent manner. We also showed that this ATP-dependent protease activity is essential for PrkA function in sporulation since mutation in the Walker A motif leads to a sporulation defect. Furthermore, we found that PrkA protease activity is tightly regulated by phosphorylation events involving one of the Ser/Thr protein kinases of B. subtilis, PrkC. Taken together, our results clarify the key role of PrkA in the complex process of B. subtilis sporulation.

Chryseobacterium caseinilyticum sp. nov., a casein hydrolyzing bacterium isolated from rice plant and emended description of Chryseobacterium piscicola

A novel Gram-stain-negative, aerobic, asporogenous, catalase-positive and oxidase-negative, non-motile, golden-yellow pigmented, rod-shaped bacterium with casein-degrading ability, designated strain GCR10^T, was isolated from roots of rice plants collected from a paddy field near Dongguk University, Republic of Korea. The results of subsequent 16S rRNA gene sequence analysis indicated that GCR10^T shares the highest sequence identity with Chryseobacterium piscicola VQ-6316s^T (98.3%). Strain GCR10^T grew at 2-32 °C (optimum, 25 °C), at pH 6.0-8.0 (optimum, pH 7.0) and in the presence of 0-2.0% (w/v) NaCl (optimum in the absence of NaCl). The novel strain was able to produce carotenoid and flexirubin-type pigments. The predominant menaquinone was MK-6 and the major fatty acids were identified as iso-C_{15 : 0}, iso-C_{17 : 0} 3-OH and iso-C_{17 : 1}ω9c. The polar lipids were phosphatidylethanolamine, four unidentified aminoglycolipids, two unidentified aminolipids and two unidentified glycolipids. The genome of GCR10^T is 4.3 Mb in length with a DNA G+C content of 36.5 mol%. Average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values between GCR10^T and Chryseobacterium piscicola VQ-6316s^T were 82.1, 25.2 and 84.3 %, respectively, which clearly indicates that the novel strain is distinct from its closest relative. The demand for natural biodegradable pigments isolated frominsects, plants or microorganisms is increasing day by day because of their beneficial pharmacological properties. Here, we describe a novel strain that produces two types of pigment, carotenoid and flexirubin. On the basis of the results from phenotypic, genotypic and chemotaxonomic analyses, strain GCR10^T represents a novel species of the genus Chryseobacterium, and the name Chryseobacterium caseinilyticum sp. nov. is proposed. The type strain is GCR10^T (=KACC 21707^T=NBRC 114715^T).

Antibiotic Sensitivity Profiling and Virulence Potential of Campylobacter jejuni Isolates from Estuarine Water in the Eastern Cape Province, South Africa

Campylobacter jejuni (CJ) is a zoonotic microbe and a major causative organism of diarrheal infection in humans that often has its functional characteristics inactivated in stressed conditions. The current study assessed the correlation between recovered CJ and water quality parameters and the drug sensitivity patterns of the pathogen to frontline antibiotics in human and veterinary medicine. Water samples (n = 244) from rivers/estuarines were collected from April⁻September 2016, and physicochemical conditions were recorded on-site. CJ was isolated from the samples using standard microbiological methods and subjected to sensitivity testing to 10 antibiotics. Mean CJ counts were between 1 and 5 logs (CFU/mL). Ninety-five isolates confirmed as CJ by PCR showed varying rates of resistance. Sensitivity testing showed resistance to tetracycline (100%), azithromycin (92%), clindamycin (84.2%), clarithromycin and doxycycline (80%), ciprofloxacin (77.8%), vancomycin (70.5%), erythromycin (70%), metronidazole (36.8%) and nalidixic acid (30.5%). Virulence encoding genes were detected in the majority 80/95, 84.2%) of the confirmed isolates from cdtB; 60/95 (63.2%) from cstII; 49/95 (51.6%) from cadF; 45/95 (47.4%) from clpP; 30/95 (31.6%) from htrB, and 0/95 (0%) from csrA. A multiple resistance cmeABC active efflux pump system was present in 69/95 (72.6) isolates. The presence of CJ was positively correlated with temperature (r = 0.17), pH (r = 0.02), dissolved oxygen (r = 0.31), and turbidity (r = 0.23) but negatively correlated with salinity (r = −0.39) and conductivity (r = −0.28). The detection of multidrug resistant CJ strains from estuarine water and the differential gene expressions they possess indicates a potential hazard to humans. Moreover, the negative correlation between the presence of the pathogen and physicochemical parameters such as salinity indicates possible complementary expression of stress tolerance response mechanisms by wild-type CJ strains.

A systems biology approach to investigate the response of Synechocystis sp. PCC6803 to a high salt environment

Background

Salt overloading during agricultural processes is causing a decrease in crop productivity due to saline sensitivity. Salt tolerant cyanobacteria share many cellular characteristics with higher plants and therefore make ideal model systems for studying salinity stress. Here, the response of fully adapted Synechocystis sp. PCC6803 cells to the addition of 6% w/v NaCl was investigated using proteomics combined with targeted analysis of transcripts.

Results

Isobaric mass tagging of peptides led to accurate relative quantitation and identification of 378 proteins, and approximately 40% of these were differentially expressed after incubation in BG-11 media supplemented with 6% salt for 9 days. Protein abundance changes were related to essential cellular functional alterations. Differentially expressed proteins involved in metabolic responses were also analysed using the probabilitistic tool Mixed Model on Graphs (MMG), where the role of energy conversion through glycolysis and reducing power through pentose phosphate pathway were highlighted. Temporal RT-qPCR experiments were also run to investigate protein expression changes at the transcript level, for 14 non-metabolic proteins. In 9 out of 14 cases the mRNA changes were in accordance with the proteins.

Conclusion

Synechocystis sp. PCC6803 has the ability to regulate essential metabolic processes to enable survival in high salt environments. This adaptation strategy is assisted by further regulation of proteins involved in non-metabolic cellular processes, supported by transcriptional and post-transcriptional control. This study demonstrates the effectiveness of using a systems biology approach in answering environmental, and in particular, salt adaptation questions in Synechocystis sp. PCC6803

From bacterial genome to functionality; case bifidobacteria

The availability of complete bacterial genome sequences has significantly furthered our understanding of the genetics, physiology and biochemistry of the microorganisms in question, particularly those that have commercially important applications. Bifidobacteria are among such microorganisms, as they constitute mammalian commensals of biotechnological significance due to their perceived role in maintaining a balanced gastrointestinal (GIT) microflora. Bifidobacteria are therefore frequently used as health-promoting or probiotic components in functional food products. A fundamental understanding of the metabolic activities employed by these commensal bacteria, in particular their capability to utilize a wide range of complex oligosaccharides, can reveal ways to provide in vivo growth advantages relative to other competing gut bacteria or pathogens. Furthermore, an in depth analysis of adaptive responses to nutritional or environmental stresses may provide methodologies to retain viability and improve functionality during commercial preparation, storage and delivery of the probiotic organism.

Contribution of conserved ATP-dependent proteases of Campylobacter jejuni to stress tolerance and virulence

In prokaryotic cells the ATP-dependent proteases Lon and ClpP (Clp proteolytic subunit) are involved in the turnover of misfolded proteins and the degradation of regulatory proteins, and depending on the organism, these proteases contribute variably to stress tolerance. We constructed mutants in the lon and clpP genes of the food-borne human pathogen Campylobacter jejuni and found that the growth of both mutants was impaired at high temperature, a condition known to increase the level of misfolded protein. Moreover, the amounts of misfolded protein aggregates were increased when both proteases were absent, and we propose that both ClpP and Lon are involved in eliminating misfolded proteins in C. jejuni. In order to bind misfolded protein, ClpP has to associate with one of several Clp ATPases. Following inactivation of the ATPase genes clpA and clpX, only the clpX mutant displayed the same heat sensitivity as the clpP mutant, indicating that the ClpXP proteolytic complex is responsible for the degradation of heat-damaged proteins in C. jejuni. Notably, ClpP and ClpX are required for growth at 42 degrees C, which is the temperature of the intestinal tract of poultry, one of the primary carriers of C. jejuni. Thus, ClpP and ClpX may be suitable targets of new intervention strategies aimed at reducing C. jejuni in poultry production. Further characterization of the clpP and lon mutants revealed other altered phenotypes, such as reduced motility, less autoagglutination, and lower levels of invasion of INT407 epithelial cells, suggesting that the proteases may contribute to the virulence of C. jejuni.

Exploiting Bifidobacterium genomes: the molecular basis of stress response

Bifidobacteria represent important human commensals because of their perceived contribution to the maintenance of a balanced gastro intestinal tract (GIT). In recent years bifidobacteria have drawn much scientific attention because of their use as live bacteria in numerous food preparations with various health-related claims. For such reasons these bacteria constitute a growing area of interest with respect to genomics, molecular biology and genetics. This review will discuss the current knowledge on the molecular players that allow bifidobacteria to contend with heat-, osmotic-, bile-and acidic stress. Here, we describe the principal molecular chaperones involved in such stresses, as well as their use as phylogenetic markers for gaining insight into the evolutionary history of high G+C Gram positive bacteria.

How high G+C Gram-positive bacteria and in particular bifidobacteria cope with heat stress: protein players and regulators

The Actinobacteridae group of bacteria includes pathogens, plant commensals, endosymbionts as well as inhabitants of the gastrointestinal tract. For various reasons, these microorganisms represent a growing area of interest with respect to genomics, molecular biology and genetics. This review will discuss the current knowledge on the molecular players that allow actinobacteria to contend with heat stress, with an emphasis on bifidobacteria. We describe the principal molecular chaperones involved in heat stress. Temporal expression of heat-shock genes based on functional genomics in members of the Actinobacteridae group is also discussed, as well as the emerging molecular mechanisms controlling the heat-stress response.

MOLECULAR AND EVOLUTIONARY BASIS OF THE CELLULAR STRESS RESPONSE

The cellular stress response is a universal mechanism of extraordinary physiological/pathophysiological significance. It represents a defense reaction of cells to damage that environmental forces inflict on macromolecules. Many aspects of the cellular stress response are not stressor specific because cells monitor stress based on macromolecular damage without regard to the type of stress that causes such damage. Cellular mechanisms activated by DNA damage and protein damage are interconnected and share common elements. Other cellular responses directed at re-establishing homeostasis are stressor specific and often activated in parallel to the cellular stress response. All organisms have stress proteins, and universally conserved stress proteins can be regarded as the minimal stress proteome. Functional analysis of the minimal stress proteome yields information about key aspects of the cellular stress response, including physiological mechanisms of sensing membrane lipid, protein, and DNA damage; redox sensing and regulation; cell cycle control; macromolecular stabilization/repair; and control of energy metabolism. In addition, cells can quantify stress and activate a death program (apoptosis) when tolerance limits are exceeded.

clpC and clpP1P2 gene expression in Corynebacterium glutamicum is controlled by a regulatory network involving the transcriptional regulators ClgR and HspR as well as the ECF sigma factor sigmaH

The ATP-dependent protease Clp plays important roles in the cell's protein quality control system and in the regulation of cellular processes. In Corynebacterium glutamicum, the levels of the proteolytic subunits ClpP1 and ClpP2 as well as of the corresponding mRNAs were drastically increased upon deletion of the clpC gene, coding for a Clp ATPase subunit. We identified a regulatory protein, designated ClgR, binding to a common palindromic sequence motif in front of clpP1P2 as well as of clpC. Deletion of clgR in the DeltaclpC background completely abolished the increased transcription of both operons, indicating that ClgR activates transcription of these genes. ClgR activity itself is probably controlled via ClpC-dependent regulation of its stability, as ClgR is only present in DeltaclpC and not in wild-type cells, whereas the levels of clgR mRNA are comparable in both strains. clpC, clpP1P2 and clgR expression is induced upon severe heat stress, however, independently of ClgR. Identification of the heat-responsive transcriptional start sites in front of these genes revealed the presence of sequence motifs typical for sigmaECF-dependent promoters. The ECF sigma factor sigmaH could be identified as being required for transcriptional activation of clpC, clpP1P2 and clgR in response to severe heat stress. A second heat-responsive but sigmaH-independent promoter in front of clgR could be identified that is subject to negative regulation by the transcriptional repressor HspR. Taken together, these results show that clpC and clpP1P2 expression in C. glutamicum is subject to complex regulation via both independent and hierarchically organized pathways, allowing for the integration of multiple environmental stimuli. Both the ClgR- and sigmaH-dependent regulation of clpC and clpP1P2 expression appears to be conserved in other actinomycetes.

An improved cloning vector for construction of gene replacements in Listeria monocytogenes

Listeria monocytogenes is a gram-positive, facultative intracellular bacterium implicated in severe food-borne illness (listeriosis) in humans. The construction of well-defined gene replacements in the genome of L. monocytogenes has been instrumental to several genetic studies of the virulence and other attributes of the organism. Construction of such mutations by currently available procedures, however, tends to be labor intensive, and gene replacement mutants are sometimes difficult to recover due to lack of direct selection for the construct. In this study we describe the construction and use of plasmid vector pGF-EM, which can be conjugatively transferred from Escherichia coli S17-1 to L. monocytogenes and which provides the genetic means for direct selection of gene replacements.