Function of Genetic Material: Progressive Insight into Antimicrobial Peptides and their Transcriptional Regulation

Metagenomics, the study of genetic material recovered directly from environmental samples, has the potential to provide insight into the structure and function of heterogeneous microbial communities. There has been an increased use of metagenomics to discover and understand the diverse biosynthetic capacities of marine microbes, thereby allowing them to be exploited for industrial, food, and health care products. This ELIXIR pilot action was motivated by the need to establish dedicated data resources and harmonized metagenomics pipelines for the marine domain, in order to enhance the exploration and exploitation of marine genetic resources. In this paper, we summarize some of the results from the ELIXIR pilot action “Marine metagenomics – towards user centric services”.

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Regulation of the CRISPR-Associated Genes by Rv2837c (CnpB) via an Orn-Like Activity in Tuberculosis Complex Mycobacteria

Journal of Bacteriology ◽

10.1128/jb.00743-17 ◽

2018 ◽

Vol 200 (8) ◽

Cited By ~ 5

Author(s):

Yang Zhang ◽

Jun Yang ◽

Guangchun Bai

Keyword(s):

Transcriptional Regulation ◽

Adaptive Immunity ◽

Parent Strain ◽

Tuberculosis Complex ◽

Content Type ◽

Multifunctional Protein ◽

Type Iii ◽

Associated Proteins ◽

Cyclic Dinucleotides ◽

Insight Into

ABSTRACT Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated proteins (Cas) provide bacteria and archaea with adaptive immunity to specific DNA invaders. Mycobacterium tuberculosis encodes a type III CRISPR-Cas system that has not been experimentally explored. In this study, we found that the CRISPR-Cas systems of both M. tuberculosis and Mycobacterium bovis BCG were highly upregulated by deletion of Rv2837c ( cnpB ), which encodes a multifunctional protein that hydrolyzes cyclic di-AMP (c-di-AMP), cyclic di-GMP (c-di-GMP), and nanoRNAs (short oligonucleotides of 5 or fewer residues). By using genetic and biochemical approaches, we demonstrated that the CnpB-controlled transcriptional regulation of the CRISPR-Cas system is mediated by an Orn-like activity rather than by hydrolyzing the cyclic dinucleotides. Additionally, our results revealed that tuberculosis (TB) complex mycobacteria are functional in processing CRISPR RNAs (crRNAs), which are also more abundant in the Δ cnpB strain than in the parent strain. The elevated crRNA levels in the Δ cnpB strain could be partially reduced by expressing Escherichia coli orn . Our findings provide new insight into transcriptional regulation of bacterial CRISPR-Cas systems. IMPORTANCE Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated proteins (Cas) provide adaptive immunity to specific DNA invaders. M. tuberculosis encodes a type III CRISPR-Cas system that has not been experimentally explored. In this study, we first demonstrated that the CRISPR-Cas systems in tuberculosis (TB) complex mycobacteria are functional in processing CRISPR RNAs (crRNAs). We also showed that Rv2837c (CnpB) controls the expression of the CRISPR-Cas systems in TB complex mycobacteria through an oligoribonuclease (Orn)-like activity, which is very likely mediated by nanoRNA. Since little is known about regulation of CRISPR-Cas systems, our findings provide new insight into transcriptional regulation of bacterial CRISPR-Cas systems.

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Same agent, different messages: insight into transcriptional regulation by SIN3 isoforms

Epigenetics & Chromatin ◽

10.1186/s13072-018-0188-y ◽

2018 ◽

Vol 11 (1) ◽

Cited By ~ 14

Author(s):

Ashlesha Chaubal ◽

Lori A. Pile

Keyword(s):

Transcriptional Regulation ◽

Insight Into

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Antimicrobial activity of human islet amyloid polypeptides: an insight into amyloid peptides’ connection with antimicrobial peptides

Biological Chemistry ◽

10.1515/hsz-2012-0107 ◽

2012 ◽

Vol 393 (7) ◽

pp. 641-646 ◽

Cited By ~ 16

Author(s):

Lan Wang ◽

Qian Liu ◽

Jin-Chun Chen ◽

Yi-Xian Cui ◽

Bing Zhou ◽

...

Keyword(s):

Antimicrobial Activity ◽

Antimicrobial Peptides ◽

Lipid Membrane ◽

Human Islet ◽

Amyloid Peptide ◽

Islet Amyloid ◽

Amyloid Peptides ◽

Amyloid Polypeptides ◽

New Evidence ◽

Insight Into

Abstract Human islet amyloid polypeptide (hIAPP) shows an antimicrobial activity towards two types of clinically relevant bacteria. The potency of hIAPP varies with its aggregation states. Circular dichroism was employed to determine the interaction between hIAPP and bacteria lipid membrane mimic. The antimicrobial activity of each aggregate species is associated with their ability to induce membrane disruption. Our findings provide new evidence revealing the antimicrobial activity of amyloid peptide, which suggest a possible connection between amyloid peptides and antimicrobial peptides.

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CryoEM structure of the type IVa pilus secretin required for natural competence in Vibrio cholerae

Nature Communications ◽

10.1038/s41467-020-18866-y ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Sara J. Weaver ◽

Davi R. Ortega ◽

Matthew H. Sazinsky ◽

Triana N. Dalia ◽

Ankur B. Dalia ◽

...

Keyword(s):

Antibiotic Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Vibrio Cholerae ◽

Natural Transformation ◽

Domain Architecture ◽

Genetic Material ◽

Surface Binding ◽

Exogenous Dna ◽

Insight Into

Abstract Natural transformation is the process by which bacteria take up genetic material from their environment and integrate it into their genome by homologous recombination. It represents one mode of horizontal gene transfer and contributes to the spread of traits like antibiotic resistance. In Vibrio cholerae, a type IVa pilus (T4aP) is thought to facilitate natural transformation by extending from the cell surface, binding to exogenous DNA, and retracting to thread this DNA through the outer membrane secretin, PilQ. Here, we use a functional tagged allele of VcPilQ purified from native V. cholerae cells to determine the cryoEM structure of the VcPilQ secretin in amphipol to ~2.7 Å. We use bioinformatics to examine the domain architecture and gene neighborhood of T4aP secretins in Proteobacteria in comparison with VcPilQ. This structure highlights differences in the architecture of the T4aP secretin from the type II and type III secretion system secretins. Based on our cryoEM structure, we design a series of mutants to reversibly regulate VcPilQ gate dynamics. These experiments support the idea of VcPilQ as a potential druggable target and provide insight into the channel that DNA likely traverses to promote the spread of antibiotic resistance via horizontal gene transfer by natural transformation.

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