PpCas9 from Pasteurella pneumotropica - a compact Type II-C Cas9 ortholog active in human cells.

CRISPR-Cas defense systems opened up the field of genome editing due to the ease with which effector Cas nucleases can be programmed with guide RNAs to access desirable genomic sites. Type II-A SpCas9 from Streptococcus pyogenes was the first Cas9 nuclease used for genome editing and it remains the most popular enzyme of its class. Nevertheless, SpCas9 has some drawbacks including a relatively large size and restriction to targets flanked by an 'NGG' PAM sequence. The more compact Type II-C Cas9 orthologs can help to overcome the size limitation of SpCas9. Yet, only a few Type II-C nucleases were fully characterized to date. Here, we characterized two Cas9 II-C orthologs, DfCas9 from Defluviimonas sp.20V17 and PpCas9 from Pasteurella pneumotropica. Both DfCas9 and PpCas9 cleave DNA in vitro and have novel PAM requirements. Unlike DfCas9, the PpCas9 nuclease is active in human cells. This small nuclease requires an 'NNNNRTT' PAM orthogonal to that of SpCas9 and thus potentially can broaden the range of Cas9 applications in biomedicine and biotechnology.

DNA targeting by Clostridium cellulolyticum CRISPR-Cas9 Type II-C system.

Type II CRISPR-Cas9 RNA-guided nucleases are widely used for genome engineering. Type II-A SpCas9 protein from Streptococcus pyogenes is the most investigated and highly used enzyme of its class. Nevertheless, it has some drawbacks, including a relatively big size, imperfect specificity and restriction to DNA targets flanked by an NGG PAM sequence. Cas9 orthologs from other bacterial species may provide a rich and largely untapped source of biochemical diversity, which can help to overcome the limitations of SpCas9. Here, we characterize CcCas9, a Type II-C CRISPR nuclease from Clostridium cellulolyticum H10. We show that CcCas9 is an active endonuclease of comparatively small size that recognizes a novel two-nucleotide PAM sequence. The CcCas9 can potentially broaden the existing scope of biotechnological applications of Cas9 nucleases and may be particularly advantageous for genome editing of C. cellulolyticum H10, a bacterium considered to be a promising biofuel producer.

Comparative analysis of Aliivibrio logei luxR1 and luxR2 genes regulation in Escherichia coli cells.

Regulation of Aliivibrio logei luxR1 and luxR2 genes was evaluated in Escherichia coli cells with use of transcriptional fusions of luxR1 and luxR2 promoter/operator regions with the Photorhabdus luminescens luxCDABE reporter gene cassette. Expression of the luxR1 and luxR2 genes was shown to largely depend on the CRP as activator. The hns::kan mutation increases the expression of luxR2 gene by two to three orders of magnitude and luxR1 gene by two to threefold. The LuxR1 and LuxR2 proteins in the presence of autoinducer (N-acyl homoserine lactone, AI) separately as well as together considerably enhanced the transcription of the luxR2 gene. In contrast, the transcription of luxR1 gene decreases depending on AI concentration in the presence of the luxR1 and luxR2 genes combination. It was identified that the promoter region of luxR2 gene consists of two promoters: Pcrp is located downstream of the crp box and Plux-box is located between the crp box and the lux box.

Antirestriction activities of KlcA (RP4) and ArdB (R64) proteins.

Antirestriction proteins of the ArdB group (ArdB, KlcA) specifically inhibit restriction (endonuclease) activity of restriction-modification (RM) type I systems. Antirestriction activity of KlcA and ArdB, encoded in transmissible plasmids RP4 (IncPα) and R64 (IncI1), respectively, has been determined. We show that the protein KlcA (RP4), an amino acid sequence identical to that of the protein KlcA (RK2), inhibits the activity of EcoKI when the klcA gene is located on the plasmid under the control of strong promoter. It was demonstrated that proteins KlcA (RP4) and ArdB (R64) are characterized by approximately equal antirestriction activity. Analysis of amino acid sequences of ArdB homologs revealed four groups of conserved amino acids located on the surface of the protein globule: (1) R16, E32, W51; (2) Y46, G48; (3) S84, D86, E132 and (4) N77, L140, D141. It was shown that substitution of polar amino acids to hydrophobic A and L leads to a significant decrease in the ArdB antirestriction activity level (approximately 100-fold). A conserved region forming a 'ring belt' on the globule surface consisting of E32, S84, E132, and both N77 and D141 as the 'key section' of ArdB/KlcA was identified.

The DNA-mimic antirestriction proteins ArdA ColIB-P9, Arn T4, and Ocr T7 as activators of H-NS-dependent gene transcription.

The antirestriction proteins ArdA ColIb-P9, Arn T4 and Ocr T7 specifically inhibit type I and type IV restriction enzymes and belong to the family of DNA-mimic proteins because their three-dimensional structure is similar to the double-helical B-form DNA. It is proposed that the DNA-mimic proteins are able to bind nucleoid protein H-NS and alleviate H-NS-silencing of the transcription of bacterial genes. Escherichia coli lux biosensors were constructed by inserting H-NS-dependent promoters into a vector, thereby placing each fragment upstream of the promoterless Photorhabdus luminescens luxCDABE operon. It was demonstrated that the DNA-mimic proteins ArdA, Arn and Ocr activate the transcription of H-NS-dependent promoters of the lux operon of marine luminescent bacteria (mesophilic Aliivibrio fischeri and psychrophilic Aliivibrio logei), and the dps gene from E. coli. It was also demonstrated that the ArdA antirestriction protein, the genes of which are located on transmissive plasmids ColIb-P9, R64, PK101, decreases levels of H-NS silencing of the PluxC promoter during conjugation in the recipient bacteria.

A combination of luxR1 and luxR2 genes activates Pr-promoters of psychrophilic Aliivibrio logei lux-operon independently of chaperonin GroEL/ES and protease Lon at high concentrations of autoinducer.

UNLABELLED: Lux-operon of psychrophilic bacteria Aliivibrio logei contains two copies of luxR and is regulated by Type I quorum sensing (QS). Activation of lux-operon of psychrophilic bacteria A. logei by LuxR1 requires about 100 times higher concentrations of autoinducer (AI) than the activation by LuxR2. On the other hand, LuxR1 does not require GroEL/ES chaperonin for its folding and cannot be degraded by protease Lon, while LuxR2 sensitive to Lon and requires GroEL/ES. Here we show that at 10(-5) - 10(-4)М concentrations of AI a combination of luxR1 and luxR2 products is capable of activating the Pr-promoters of A. logei lux-operon in Escherichia coli independently of GroEL/ES and protease Lon. The presence of LuxR1 assists LuxR2 in gro(-) cells when AI was added at high concentration, while at low concentration of AI in a cell LuxR1 decreases the LuxR2 activity. These observations may be explained by the formation of LuxR1/LuxR2 heterodimers that act in complex with AI independently from GroEL/ES and protease Lon. IMPORTANCE: This study expands current understanding of QS regulation in A. logei as it implies cooperative regulation of lux-operon by LuxR1 and LuxR2 proteins.

Lux-operon of the marine psychrophilic bacterium Aliivibrio logei: a comparative analysis of the LuxR1/LuxR2 regulatory activity in Escherichia coli cells.

The lux-operon of the psychrophilic bioluminescent bacterium Aliivibrio logei is regulated by quorum sensing (QS). The key components of this system are LuxI, which catalyses synthesis of the autoinducer (AI), and LuxR, which activates transcription of the entire lux-operon. The lux-operon of A. logei contains two copies of the luxR gene: luxR1 and luxR2. In the present study, lux-operon sequence analysis from 16 strains of A. logei, isolated from cold habitats of the White, Baltic, Okhotsk and Bering seas, was carried out. Phylogenetic analysis showed that all isolated strains of A. logei have both copies of luxR genes which are homologous to luxR genes of the related Aliivibrio salmonicida. Evaluation of LuxR1 and LuxR2 activity showed that LuxR2 remains active at significantly lower concentrations of AI (10- 9 M) than LuxR1, which is active only at high AI concentrations (10- 6 M). As the QS response is already prominent at AI concentrations as low as 10- 8 to 10- 9 M, we conclude that LuxR2 is the main activator of the lux-operon of A. logei. The thermolabilities of LuxR1 and LuxR2 are similar and exceed that of LuxR of the mesophilic bacterium Aliivibrio fischeri. In contrast to LuxR2, LuxR1 is not a substrate of Lon protease and does not require the chaperonin GroEL/ES for its folding. This study expands our current understanding of QS regulation in A. logei as it implies differential regulation by LuxR1 and LuxR2 proteins.