Defense strategies of bacteria

1. BACTERIAL DEFENSE SYSTEM
DR. CHAYANIKA DAS
Ph.D
DIVISION OF VETERINARY MICROBIOLOGY

2. INTRODUCTION

3. Each step can be targeted for anti-phage mechanisms
BACTERIOPHAGE AND ITS LIFE CYCLE
Seed et al., 2015

4. DEFENCE STRATEGIES OF BACTERIA
Resistance based on
viral receptor variation
Immunity
Dormancy induction
& programmed cell
death
Blocking phage
receptors,
Production of
extracellular matrix,
Masking receptors
Innate: RM system,
Phage exclusion,
pAgo system
Adaptive:CRISPR-Cas,
Toxin-antitoxin
system
Abortive infection
system
Koonin et al., 2017

5. PHASE VARIATION
PREVENTING PHAGE ADSORPTION
Chaturongakul and Ounjai, 2014; Kim and Ryu, 2012
Phage receptors in Salmonella

6. Phage T5 receptors
Lipoprotein (Llp)
PREVENTING PHAGE ADSORPTION
Labrie et al., 2010

7. PHAGE EXCLUSION
Pgl W Pgl X Pgl Y Pgl Z
Pgl system of Streptomyces coelicolor
Bacteriophage exclusion
(BREX)
Chaudhary, 2017
Protein kinase Methyl transferase unknown Alkaline phosphatase

8. PHAGE EXCLUSION
DNA injection
BREX system
Lacking BREX
system
DNA replication
Transcription &
translation
Assembly
Lysis
Integration of
Phage DNA
TAGGAC
CH₃
Blocking of replication
and integration of phage
DNA by BREX system
Chaudhary, 2017

9. RESTRICTION MODIFICATION
Subunit composition
Sequence
recognition
Cleavage position
Cofactor
requirement
Substrate specificity
4 types
Type I Type II Type III Type IV
Vasu and Nagaraja, 2013
Salvatore Luria(1952) &
Mary Human (1953)

10. microbewiki.kenyon.edu
RESTRICTION MODIFICATION
enzymes
sites

11. Argonaute centered RNA/DNA – Guided defense
Argonaute (Ago) proteins RNA interference
(RNAi) pathway
Prokaryotic Argonaute (pAgo) proteins: PIWI superfamily
Swarts et al., 2014

12. Swarts et al., 2014
p-TGAGGTAGTAGGTTGTATAGT
GCUCCAUCAUCC
Guide DNA
Target RNA
5’
3’
3’
5’
1 10 21
1’ 10’ 12’

13. CRISPR- Cas SYSTEM
1993:
Characterization of
CRISPR locus
2005:
Identification of
Cas9 gene

14. CRISPR- Cas SYSTEM (Contd...)
Hille and Charpentier, 2016
PAM

15. CRISPR- Cas SYSTEM (Contd...)
doudnalab.org
PAM

16. Toxin-antitoxin system
Schuster and Bertram, 2013; Wen et al., 2014
•Toxin (proteins)
•Anti-toxin (proteins/small RNA)
ccdAB- the first TA being identified
Classes of Toxin-antitoxin system and their mode of action
Hok-sok TA system

17. Schuster and Bertram, 2013; Wen et al., 2014
First type III TA system:
ToxIN TA system in
Pectobacterium atrosepticumm
First type II TA system:
MazF-MazE system in
Escherichia coli

18. Schuster and Bertram, 2013; Wen et al., 2014
CbtA
MreB FtsZ
CbeA
GhoT
GhoS
Cell death
or persistent
ghost cells
Rescue cell growth
E. coli K12
Cell division
Arrest
Rescue
E. coli

19. ABORTIVE INFECTION
Altruistic cell
suicidal death
systems
Limit viral
replication with
toxic proteins
Bifunctionality
of TA system
Short et al., 2018
Pectobacterium atrosepticum (Type III TA system)

20. Evolutionary consequences of battling interactions between
Phage and bacteria
•The extensive co-evolution of both phage and host has resulted in considerable diversity
on the part of both bacterial and phage defensive and offensive strategies
•A reservoir of novel defense mechanisms lies in the most variable regions of bacterial
genomes, known as genomic islands
• A strategy that focuses on such islands to search for novel phage resistance mechanisms
might lead, in the future, to surprising discoveries
Stern and Sorek, 2011

21. Defense island
DISARM
system associated with restriction modification
Class 1 DISARM
Class 2 DISARM
Core genes
Ofir et al., 2017

22. DISARM
Ofir et al., 2017
DISARM confers protection against multiple phage types
DISARM allows phage adsorption but prevents phage replication
Essential components for DISARM anti-phage activity
drmMII methylates the DNA at CCWGG motifs and its absence leads to
DISARM toxicity
Bacillus
subtilis
BEST7003

23. The existence of an R/M-related active methyltransferase, the
toxicity caused by its deletion, and the depletion of phage DNA
during infection suggest that DISARM represents a new
composition of R/M system that differs from other known such
systems
Ofir et al., 2017

24. DEFENSE SYSTEM: A BURDEN OR BENIFIT
 A benifit to the bacterial population
 A burden for the phages
 As phage and bacteria have a long co-evolutionary history, we can assume that
phages can effectively raise a counterresistance, through various means to cope
with such selective forces
 Phages cause a shift of the balance in the mutually benifited ecosystem of gut
microbiota of human and animals via their introduction into the bacterial
genome, and expression of phage genes dramatically changing bacterial
phenotypes and thus contributes to a burden of disease to the mammalian
population
 Contamination of phages in processed food: a burden in the field of
Biotechnology and Food industries
 Empowerment of the bacterial defense system is associated with antimicrobial
resistance posing the biggest burden to the human and animal population today
Samson and Moineau, 2013; Seed et al., 2015; Zhou et al., 2015

25. THE CONCLUSION
•Bacteria are constantly threatened with predation by bacteriophages, which
are estimated to outnumber their bacterial hosts
•In response, bacteria have evolved several defense mechanisms to protect
themselves against phage infection
•These mechanisms can be subsequently countered by evolved phage mutants,
resulting in an “arms race” of antagonistic co-evolution of bacteria and phage
•Many more phage resistance barriers are likely to be uncovered, as these
natural antiviral systems reflect the remarkable diversity of bacterial viruses and
the role of resistance in maintaining the phage–host balance in either natural or
man-made environments
•Bacteria are constantly threatened with predation by bacteriophages, which
are estimated to outnumber their bacterial hosts
•In response, bacteria have evolved several defense mechanisms to protect
themselves against phage infection
•These mechanisms can be subsequently countered by evolved phage mutants,
resulting in an “arms race” of antagonistic co-evolution of bacteria and phage
•Many more phage resistance barriers are likely to be uncovered, as these
natural antiviral systems reflect the remarkable diversity of bacterial viruses and
the role of resistance in maintaining the phage–host balance in either natural or
man-made environments

26. 1. Seed KD (2015); Battling Phages: How Bacteria Defend against Viral Attack; PLoS
Pathog ; 11(6)
2. Kawa et al., 2012: Learning from Bacteriophages - Advantages and Limitations of
Phage and Phage-Encoded Protein Applications; Current Protein and Peptide Science;
13, 699-722
3. Chaturongakul and Ounjai, 2014; Phage–host interplay :examples from tailed phages
and Gram-negative bacterial pathogens; Frontiers in Mibrociology; doi: 10.3389/
fmicb.2014.00442
4. Kim and Ryu, 2012; Spontaneous and transient defence against bacteriophage by
phase-variable glucosylation of O-antigen in Salmonella enterica serovar
Typhimurium; Molecular Microbiology; 86(2), 411–425
5. Labrie et al., 2010; Bacteriophage resistance mechanisms; Natures Reviews
Microbiology; Vol 8, (317-327)
6. Chaudhary, 2017; BacteRiophage EXclusion (BREX): A novel anti-phage mechanism in
the arsenal of bacterial defense system; J Cell Physiol.; 233:771–773
7. Vasu and Nagaraja, 2013; Diverse Functions of Restriction-Modification Systems in
Addition to Cellular Defense; Microbiology and Molecular Biology Reviews; vol 77:
53–72
8. https://microbewiki.kenyon.edu/index.php/File:Delete3.png
References

27. 9. Swarts et al., 2014; The evolutionary journey of Argonaute proteins; Nature
Structural & Molecular Biology; Vol 21: 743-753
10. Koonin et al., 2017; Evolutionary Genomics of Defense Systems in Archaea and
Bacteria; Annu. Rev. Microbiol.; 71:233–61
11. Hille and Charpentier, 2016; CRISPR-Cas: biology, mechanisms and relevance; Phil.
Trans. R. Soc.; 371:0496
12. Schuster and Bertram, 2013; Toxin–antitoxin systems are ubiquitous and versatile
modulators of prokaryotic cell fate; FEMS Microbiol Lett; 340: 73–85
13. Short et al., 2018; The bacterial Type III toxinantitoxin system, ToxIN, is a dynamic
protein-RNA complex with stability-dependent antiviral abortive infection activity;
Scientific reports; 8:1013
14. Ofir et al., 2017; DISARM is a widespread bacterial defence system with broad
anti-phage activities; Nature Microbiology; https://doi.org/10.1038/s41564-017-
0051-0
15. Samson and Moineau, 2013; Bacteriophages in food fermentations: new frontiers
in a continuous arms race; Annu Rev Food Sci Technol.; vol 4:347-68
16. Zhou et al., 2015; The Three Bacterial Lines of Defense against Antimicrobial
Agents; Int. J. Mol. Sci.; 16, 21711-21733

28. THANK YOU