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Survey of clustered regularly interspaced short palindromic repeats and their associated Cas proteins (CRISPR/Cas) systems in multiple sequenced strains of Klebsiella pneumoniae.

Ostria-Hernández ML, Sánchez-Vallejo CJ, Ibarra JA, Castro-Escarpulli G - BMC Res Notes (2015)

Bottom Line: The cas genes in these strains comprises eight cas genes similar to those found in Escherichia coli, suggesting they belong to the type I-E group, although their arrangement is slightly different.BLAST searches demonstrated that 38 of the 116 spacer sequences (33%) are significantly similar to either plasmid, phage or genome sequences, while the remaining 78 sequences (67%) showed no significant similarity to other sequences.The region where the CRISPR/Cas systems were located is the same in all the Klebsiella genomes containing it, it has a syntenic architecture, and is located among genes encoding for proteins likely involved in metabolism and resistance to antibiotics.

View Article: PubMed Central - PubMed

Affiliation: Laboratorio de Bacteriología Médica y, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Delegación Miguel Hidalgo, CP 11340, Mexico, D.F., Mexico. marthal_19@yahoo.com.mx.

ABSTRACT

Background: In recent years the emergence of multidrug resistant Klebsiella pneumoniae strains has been an increasingly common event. This opportunistic species is one of the five main bacterial pathogens that cause hospital infections worldwide and multidrug resistance has been associated with the presence of high molecular weight plasmids. Plasmids are generally acquired through horizontal transfer and therefore is possible that systems that prevent the entry of foreign genetic material are inactive or absent. One of these systems is CRISPR/Cas. However, little is known regarding the clustered regularly interspaced short palindromic repeats and their associated Cas proteins (CRISPR/Cas) system in K. pneumoniae. The adaptive immune system CRISPR/Cas has been shown to limit the entry of foreign genetic elements into bacterial organisms and in some bacteria it has been shown to be involved in regulation of virulence genes. Thus in this work we used bioinformatics tools to determine the presence or absence of CRISPR/Cas systems in available K. pneumoniae genomes.

Results: The complete CRISPR/Cas system was identified in two out of the eight complete K. pneumoniae genomes sequences and in four out of the 44 available draft genomes sequences. The cas genes in these strains comprises eight cas genes similar to those found in Escherichia coli, suggesting they belong to the type I-E group, although their arrangement is slightly different. As for the CRISPR sequences, the average lengths of the direct repeats and spacers were 29 and 33 bp, respectively. BLAST searches demonstrated that 38 of the 116 spacer sequences (33%) are significantly similar to either plasmid, phage or genome sequences, while the remaining 78 sequences (67%) showed no significant similarity to other sequences. The region where the CRISPR/Cas systems were located is the same in all the Klebsiella genomes containing it, it has a syntenic architecture, and is located among genes encoding for proteins likely involved in metabolism and resistance to antibiotics.

Conclusions: The CRISPR/Cas system is not widely distributed in K. pneumoniae genomes, those present most likely belong to type I-E with few differences from the arrangement of the cse3 gene and most of the spacers have not been are not described yet. Given that the CRISPR/Cas system is scarcely distributed among K. pneumoniae genomes it is not clear whether it is involved in either immunity against foreign genetic material or virulence. We consider that this study represents a first step to understand the role of CRISPR/Cas in K. pneumoniae.

No MeSH data available.


Related in: MedlinePlus

Description of direct repeats and spacer sequences found in Klebsiella pneumoniae genomes. a Logo obtained in WebLogo of the direct repeats consensus sequences of CRISPR arrays. The sequences are partially palindromic and symmetrical. b Match of spacer sequences with sequences of phages, plasmids and bacterial genomes deposited in GenBank.
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Fig3: Description of direct repeats and spacer sequences found in Klebsiella pneumoniae genomes. a Logo obtained in WebLogo of the direct repeats consensus sequences of CRISPR arrays. The sequences are partially palindromic and symmetrical. b Match of spacer sequences with sequences of phages, plasmids and bacterial genomes deposited in GenBank.

Mentions: Subsequently, and based on the comparison of the cas operon of K. pneumoniae with that of E. coli (Type I-E or CASS2), we observed that K. pneumoniae strains have the same number of genes but with a difference in the location of cse3. That is, for E. coli cse3 is located downstream of cas5e while in K. pneumoniae it is located between cse2 and cse4 (Fig. 2). Whether this rearrangement influences the formation of the CASCADE complex involved in the recognition of foreign genetic material in K. pneumoniae still unknown and a matter of future research. In order to characterize the DRs in each CRISPR sequence we performed a detailed analysis by aligning all 10 of the DRs obtained through the analysis derived from the CRISPRFinder. The consensus sequence of these DRs showed a conserved GT(C/g)TTCCCC sequence at the 5′ region and a conserved GGGG(G/a)T(G/a)(T/a) (T/a)(T/c)C at the 3′ region. The main changes were detected in the middle of the sequence (position 12 to 15). Our results show that the DR sequence was symmetrical and partially palindromic (Fig. 3). Given the immune role exerted by the CRISPR/cas system, it has been observed that the spacer sequences are derived from HGT material [28]. In order to define the origin of the spacers in the systems identified in K. pneumoniae BLASTn searches were performed. This analysis showed that 38 of the 116 spacer sequences (33%) have significant similarity to plasmids, phages or genome sequences in Klebsiella or other bacteria. The distribution of these sequences was: 13% (15/116) of the spacer sequences had similarity to genes belonging to phages, 8% (9/116) corresponded to gene sequences of plasmids, 5% (6/116) to genes of the Klebsiella spp. genome, while 7% (8/116) were similar to genes that belong to genomes of other bacteria. The remaining 78 sequences (67%) showed no significant similarity to any other sequence (Fig. 3). In addition, strains that share spacer sequences were not detected. These results show a diverse origin of the CRISPR sequences, indicating that they were probably acquired from diverse events involving the entry of foreign genetic material.Fig. 3


Survey of clustered regularly interspaced short palindromic repeats and their associated Cas proteins (CRISPR/Cas) systems in multiple sequenced strains of Klebsiella pneumoniae.

Ostria-Hernández ML, Sánchez-Vallejo CJ, Ibarra JA, Castro-Escarpulli G - BMC Res Notes (2015)

Description of direct repeats and spacer sequences found in Klebsiella pneumoniae genomes. a Logo obtained in WebLogo of the direct repeats consensus sequences of CRISPR arrays. The sequences are partially palindromic and symmetrical. b Match of spacer sequences with sequences of phages, plasmids and bacterial genomes deposited in GenBank.
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4522967&req=5

Fig3: Description of direct repeats and spacer sequences found in Klebsiella pneumoniae genomes. a Logo obtained in WebLogo of the direct repeats consensus sequences of CRISPR arrays. The sequences are partially palindromic and symmetrical. b Match of spacer sequences with sequences of phages, plasmids and bacterial genomes deposited in GenBank.
Mentions: Subsequently, and based on the comparison of the cas operon of K. pneumoniae with that of E. coli (Type I-E or CASS2), we observed that K. pneumoniae strains have the same number of genes but with a difference in the location of cse3. That is, for E. coli cse3 is located downstream of cas5e while in K. pneumoniae it is located between cse2 and cse4 (Fig. 2). Whether this rearrangement influences the formation of the CASCADE complex involved in the recognition of foreign genetic material in K. pneumoniae still unknown and a matter of future research. In order to characterize the DRs in each CRISPR sequence we performed a detailed analysis by aligning all 10 of the DRs obtained through the analysis derived from the CRISPRFinder. The consensus sequence of these DRs showed a conserved GT(C/g)TTCCCC sequence at the 5′ region and a conserved GGGG(G/a)T(G/a)(T/a) (T/a)(T/c)C at the 3′ region. The main changes were detected in the middle of the sequence (position 12 to 15). Our results show that the DR sequence was symmetrical and partially palindromic (Fig. 3). Given the immune role exerted by the CRISPR/cas system, it has been observed that the spacer sequences are derived from HGT material [28]. In order to define the origin of the spacers in the systems identified in K. pneumoniae BLASTn searches were performed. This analysis showed that 38 of the 116 spacer sequences (33%) have significant similarity to plasmids, phages or genome sequences in Klebsiella or other bacteria. The distribution of these sequences was: 13% (15/116) of the spacer sequences had similarity to genes belonging to phages, 8% (9/116) corresponded to gene sequences of plasmids, 5% (6/116) to genes of the Klebsiella spp. genome, while 7% (8/116) were similar to genes that belong to genomes of other bacteria. The remaining 78 sequences (67%) showed no significant similarity to any other sequence (Fig. 3). In addition, strains that share spacer sequences were not detected. These results show a diverse origin of the CRISPR sequences, indicating that they were probably acquired from diverse events involving the entry of foreign genetic material.Fig. 3

Bottom Line: The cas genes in these strains comprises eight cas genes similar to those found in Escherichia coli, suggesting they belong to the type I-E group, although their arrangement is slightly different.BLAST searches demonstrated that 38 of the 116 spacer sequences (33%) are significantly similar to either plasmid, phage or genome sequences, while the remaining 78 sequences (67%) showed no significant similarity to other sequences.The region where the CRISPR/Cas systems were located is the same in all the Klebsiella genomes containing it, it has a syntenic architecture, and is located among genes encoding for proteins likely involved in metabolism and resistance to antibiotics.

View Article: PubMed Central - PubMed

Affiliation: Laboratorio de Bacteriología Médica y, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Delegación Miguel Hidalgo, CP 11340, Mexico, D.F., Mexico. marthal_19@yahoo.com.mx.

ABSTRACT

Background: In recent years the emergence of multidrug resistant Klebsiella pneumoniae strains has been an increasingly common event. This opportunistic species is one of the five main bacterial pathogens that cause hospital infections worldwide and multidrug resistance has been associated with the presence of high molecular weight plasmids. Plasmids are generally acquired through horizontal transfer and therefore is possible that systems that prevent the entry of foreign genetic material are inactive or absent. One of these systems is CRISPR/Cas. However, little is known regarding the clustered regularly interspaced short palindromic repeats and their associated Cas proteins (CRISPR/Cas) system in K. pneumoniae. The adaptive immune system CRISPR/Cas has been shown to limit the entry of foreign genetic elements into bacterial organisms and in some bacteria it has been shown to be involved in regulation of virulence genes. Thus in this work we used bioinformatics tools to determine the presence or absence of CRISPR/Cas systems in available K. pneumoniae genomes.

Results: The complete CRISPR/Cas system was identified in two out of the eight complete K. pneumoniae genomes sequences and in four out of the 44 available draft genomes sequences. The cas genes in these strains comprises eight cas genes similar to those found in Escherichia coli, suggesting they belong to the type I-E group, although their arrangement is slightly different. As for the CRISPR sequences, the average lengths of the direct repeats and spacers were 29 and 33 bp, respectively. BLAST searches demonstrated that 38 of the 116 spacer sequences (33%) are significantly similar to either plasmid, phage or genome sequences, while the remaining 78 sequences (67%) showed no significant similarity to other sequences. The region where the CRISPR/Cas systems were located is the same in all the Klebsiella genomes containing it, it has a syntenic architecture, and is located among genes encoding for proteins likely involved in metabolism and resistance to antibiotics.

Conclusions: The CRISPR/Cas system is not widely distributed in K. pneumoniae genomes, those present most likely belong to type I-E with few differences from the arrangement of the cse3 gene and most of the spacers have not been are not described yet. Given that the CRISPR/Cas system is scarcely distributed among K. pneumoniae genomes it is not clear whether it is involved in either immunity against foreign genetic material or virulence. We consider that this study represents a first step to understand the role of CRISPR/Cas in K. pneumoniae.

No MeSH data available.


Related in: MedlinePlus