Accepted Manuscript Title: Genome Level Analysis of Bacteriocins of Lactic Acid Bacteria Author: Neetigyata Pratap Singh Abhay Tiwari Ankiti Bansal Shruti Thakur Garima Sharma Reema Gabrani PII: DOI: Reference:
S1476-9271(15)00030-4 http://dx.doi.org/doi:10.1016/j.compbiolchem.2015.02.013 CBAC 6405
To appear in:
Computational Biology and Chemistry
Received date: Revised date: Accepted date:
29-8-2014 9-2-2015 21-2-2015
Please cite this article as: Singh, Neetigyata Pratap, Tiwari, Abhay, Bansal, Ankiti, Thakur, Shruti, Sharma, Garima, Gabrani, Reema, Genome Level Analysis of Bacteriocins of Lactic Acid Bacteria.Computational Biology and Chemistry http://dx.doi.org/10.1016/j.compbiolchem.2015.02.013 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Genome Level Analysis of Bacteriocins of Lactic Acid Bacteria Neetigyata Pratap Singh#, Abhay Tiwari#, Ankiti Bansal, Shruti Thakur, Garima Sharma, Reema Gabrani* Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, NOIDA, India #
Both authors have contributed equally
*
Corresponding author. Tel: +91-120-2594210; Email: [email protected]
Graphical abstract
Highlights
Identification of bacteriocin secretors lactic acid bacteria and biosynthetic gene with bioinformatic tools. Phylogenetic tree of LAB with rpoB and gyrB (housekeeping genes) by MEGA6 tool. Physiochemical and secondary structure analysis of putative strains by computational methodology. ABSTRACT
Bacteriocins are antimicrobial peptides which are ribosomally synthesized by mainly all bacterial species. LABs (Lactic Acid Bacteria) are a diverse group of bacteria that include around 20 genera of various species. Though LABs have a tremendous potential for production of anti-microbial peptides, this group of bacteria is still underexplored for bacteriocins. To study the diversity among bacteriocin encoding clusters and the putative bacteriocin precursors, genome mining was performed on 20 different species of LAB not reported to be bacteriocin producers. The phylogenetic tree of gyrB, rpoB, and 16S rRNA were constructed using MEGA6 software to analyse the diversity among strains. Putative bacteriocins operons identified were found to be diverse and were further characterized on the basis of physiochemical properties and the secondary structure. The presence of at least two cysteine residues in most of the observed putative bacteriocins leads to disulphide bond formation and provide stability. Our data suggests that LABs are prolific source of low molecular weight non modified peptides.
Key words: - Bacteriocins, BAGEL3, MEGA6, ProtParam, SOPMA
1. INTRODUCTION
Bacteriocins are ribosomally synthesized antimicrobial produced by both Gram positive and Gram negative bacteria [1]. They have been shown to be active against pathogens including bacteria, either of the same species (narrow spectrum), or across genera (broad spectrum) [2]. Thus the bacteriocins help the producer bacteria to gain a competitive advantage in its niche environment to reduce the competitors to gain resources and form an important component of chemical defense system. Bacteriocins are mainly small, cationic and are composed of more than 30% hydrophobic residues [3]. The cationic charge of these peptides ensures electrostatic affinity with the negatively charged bacterial outer membrane, while the hydrophobic part of the peptide interacts with the cell membrane and enters the double lipid membrane. Bacteriocins of Gram-positive bacteria are more diverse than the bacteriocins described for the Gram-negative bacteria. Among the Gram positive bacteria, bacteriocins produced by the lactic acid bacteria (LAB) have gained particular attention nowadays [4]. LABs are generally regarded as safe (GRAS) and so are their metabolic products, bacteriocins. These substances find application in the food industry as natural preservatives and can also prove to be an effective alternative to antibiotics. Bacteriocins produced by the LAB have been categorized into three different classes according to their biochemical and genetic properties. Class I (lantibiotics) contains small peptides and unusual post-translational modified residues. Class II bacteriocins are non lantibiotics, small in size (
S1476-9271(15)00030-4 http://dx.doi.org/doi:10.1016/j.compbiolchem.2015.02.013 CBAC 6405
To appear in:
Computational Biology and Chemistry
Received date: Revised date: Accepted date:
29-8-2014 9-2-2015 21-2-2015
Please cite this article as: Singh, Neetigyata Pratap, Tiwari, Abhay, Bansal, Ankiti, Thakur, Shruti, Sharma, Garima, Gabrani, Reema, Genome Level Analysis of Bacteriocins of Lactic Acid Bacteria.Computational Biology and Chemistry http://dx.doi.org/10.1016/j.compbiolchem.2015.02.013 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Genome Level Analysis of Bacteriocins of Lactic Acid Bacteria Neetigyata Pratap Singh#, Abhay Tiwari#, Ankiti Bansal, Shruti Thakur, Garima Sharma, Reema Gabrani* Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, NOIDA, India #
Both authors have contributed equally
*
Corresponding author. Tel: +91-120-2594210; Email: [email protected]
Graphical abstract
Highlights
Identification of bacteriocin secretors lactic acid bacteria and biosynthetic gene with bioinformatic tools. Phylogenetic tree of LAB with rpoB and gyrB (housekeeping genes) by MEGA6 tool. Physiochemical and secondary structure analysis of putative strains by computational methodology. ABSTRACT
Bacteriocins are antimicrobial peptides which are ribosomally synthesized by mainly all bacterial species. LABs (Lactic Acid Bacteria) are a diverse group of bacteria that include around 20 genera of various species. Though LABs have a tremendous potential for production of anti-microbial peptides, this group of bacteria is still underexplored for bacteriocins. To study the diversity among bacteriocin encoding clusters and the putative bacteriocin precursors, genome mining was performed on 20 different species of LAB not reported to be bacteriocin producers. The phylogenetic tree of gyrB, rpoB, and 16S rRNA were constructed using MEGA6 software to analyse the diversity among strains. Putative bacteriocins operons identified were found to be diverse and were further characterized on the basis of physiochemical properties and the secondary structure. The presence of at least two cysteine residues in most of the observed putative bacteriocins leads to disulphide bond formation and provide stability. Our data suggests that LABs are prolific source of low molecular weight non modified peptides.
Key words: - Bacteriocins, BAGEL3, MEGA6, ProtParam, SOPMA
1. INTRODUCTION
Bacteriocins are ribosomally synthesized antimicrobial produced by both Gram positive and Gram negative bacteria [1]. They have been shown to be active against pathogens including bacteria, either of the same species (narrow spectrum), or across genera (broad spectrum) [2]. Thus the bacteriocins help the producer bacteria to gain a competitive advantage in its niche environment to reduce the competitors to gain resources and form an important component of chemical defense system. Bacteriocins are mainly small, cationic and are composed of more than 30% hydrophobic residues [3]. The cationic charge of these peptides ensures electrostatic affinity with the negatively charged bacterial outer membrane, while the hydrophobic part of the peptide interacts with the cell membrane and enters the double lipid membrane. Bacteriocins of Gram-positive bacteria are more diverse than the bacteriocins described for the Gram-negative bacteria. Among the Gram positive bacteria, bacteriocins produced by the lactic acid bacteria (LAB) have gained particular attention nowadays [4]. LABs are generally regarded as safe (GRAS) and so are their metabolic products, bacteriocins. These substances find application in the food industry as natural preservatives and can also prove to be an effective alternative to antibiotics. Bacteriocins produced by the LAB have been categorized into three different classes according to their biochemical and genetic properties. Class I (lantibiotics) contains small peptides and unusual post-translational modified residues. Class II bacteriocins are non lantibiotics, small in size (
