A response regulator protein with antar domain, AvnR, in Acinetobacter baumannii ATCC 17978 impacts its virulence and amino acid metabolism

Role of the NtrC family response regulator in nitrogen metabolism of Acinetobacter baumannii

Acinetobacter baumannii is an important Gram-negative nosocomial pathogen that causes opportunistic infections and employs different mechanisms to survive in the presence of antibiotics in the host. Nutrient limitation is one of the important defense mechanisms of the mammalian immune system to fight against the colonization of pathogens like A. baumannii. The present study describes an NtrC-type Response Regulator (RR) A1S_1978 involved in modulating the metabolism and cell morphology of A. baumannii via a two-component system. This RR was found to be highly conserved in the Acinetobacter and other important Gram-negative pathogens. Sequence analysis reveals that this RR contains an HTH_8 DNA-binding domain. It is also observed that deletion of this RR resulted in elongated cell phenotype and altered colony morphology of A. baumannii. We showed that the ability of A. baumannii to form biofilm and pellicle is partly abolished upon deletion of this response regulator. We showed that mutant strains lacking RR A1S_1978 have diminished growth in the absence of the nitrogen source. The transcriptome analysis of the A1S_1978 deletion mutant revealed that 253 genes were differentially expressed, including 80 genes that were upregulated by at least 2-fold and 173 genes that were down regulated in the ΔA1S_1978 strain. The transcriptome data showed an association between the A1S_1978 RR and key genes related to various nitrogen and amino acid metabolism processes, which was further confirmed by real time PCR analysis. The deletion of this RR leads to a reduction in persister cell formation against ciprofloxacin antibiotic. Taken together the results of this investigation provide significant evidence that the RR A1S_1978 is a global regulator in A. baumannii.

Comparative Transcriptomic Profiling of Pellicle and Planktonic Cells from Carbapenem-Resistant Acinetobacter baumannii

Acinetobacter baumannii forms air-liquid interface pellicles that boost its ability to withstand desiccation and increase survival under antibiotic pressure. This study aims to delve into the transcriptomic profiles of pellicle cells from clinical strains of carbapenem-resistant A. baumannii (CRAB). The total RNA was extracted from pellicle cells from three pellicle-forming CRAB strains and planktonic cells from three non-pellicle-forming CRAB strains, subject to RNA sequencing using Illumina HiSeq 2500 system. A transcriptomic analysis between pellicle and planktonic cells, along with differential expression genes (DEGs) analysis and enrichment analysis of annotated COGs, GOs, and KEGGs, was performed. Our analysis identified 366 DEGs in pellicle cells: 162 upregulated genes and 204 downregulated genes. The upregulated ABUW_1624 (yiaY) gene and downregulated ABUW_1550 gene indicated potential involvement in fatty acid degradation during pellicle formation. Another upregulated ABUW_2820 (metQ) gene, encoding the D-methionine transporter system, hinted at its contribution to pellicle formation. The upregulation of two-component systems, CusSR and KdpDE, which implies the regulation of copper and potassium ions in a CRAB pellicle formation was also observed. These findings provide valuable insights into the regulation of gene expression during the formation of pellicles in CRAB, and these are potential targets that may aid in the eradication of CRAB infections.

CRISPR-Based Gene Editing in Acinetobacter baumannii to Combat Antimicrobial Resistance

Antimicrobial resistance (AMR) poses a significant threat to the health, social, environment, and economic sectors on a global scale and requires serious attention to addressing this issue. Acinetobacter baumannii was given top priority among infectious bacteria because of its extensive resistance to nearly all antibiotic classes and treatment options. Carbapenem-resistant A. baumannii is classified as one of the critical-priority pathogens on the World Health Organization (WHO) priority list of antibiotic-resistant bacteria for effective drug development. Although available genetic manipulation approaches are successful in A. baumannii laboratory strains, they are limited when employed on newly acquired clinical strains since such strains have higher levels of AMR than those used to select them for genetic manipulation. Recently, the CRISPR-Cas (Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) system has emerged as one of the most effective, efficient, and precise methods of genome editing and offers target-specific gene editing of AMR genes in a specific bacterial strain. CRISPR-based genome editing has been successfully applied in various bacterial strains to combat AMR; however, this strategy has not yet been extensively explored in A. baumannii. This review provides detailed insight into the progress, current scenario, and future potential of CRISPR-Cas usage for AMR-related gene manipulation in A. baumannii.

Acinetobacter Metabolism in Infection and Antimicrobial Resistance

Acinetobacter infections have high rates of mortality due to an increasing incidence of infections by multidrug-resistant (MDR) and extensively-drug-resistant (XDR) strains. Therefore, new therapeutic strategies for the treatment of Acinetobacter infections are urgently needed. Acinetobacter spp. are Gram-negative coccobacilli that are obligate aerobes and can utilize a wide variety of carbon sources. Acinetobacter baumannii is the main cause of Acinetobacter infections, and recent work has identified multiple strategies A. baumannii uses to acquire nutrients and replicate in the face of host nutrient restriction. Some host nutrient sources also serve antimicrobial and immunomodulatory functions. Hence, understanding Acinetobacter metabolism during infection may provide new insights into novel infection control measures. In this review, we focus on the role of metabolism during infection and in resistance to antibiotics and other antimicrobial agents and discuss the possibility that metabolism may be exploited to identify novel targets to treat Acinetobacter infections.

OUP accepted manuscript

Regulated transcription termination provides an efficient and responsive means to control gene expression. In bacteria, rho-independent termination occurs through the formation of an intrinsic RNA terminator loop, which disrupts the RNA polymerase elongation complex, resulting in its dissociation from the DNA template. Bacteria have a number of pathways for overriding termination, one of which is the formation of mutually exclusive RNA motifs. ANTAR domains are a class of antiterminator that bind and stabilize dual hexaloop RNA motifs within the nascent RNA chain to prevent terminator loop formation. We have determined the structures of the dimeric ANTAR domain protein EutV, from Enterococcus faecialis, in the absence of and in complex with the dual hexaloop RNA target. The structures illustrate conformational changes that occur upon RNA binding and reveal that the molecular interactions between the ANTAR domains and RNA are restricted to a single hexaloop of the motif. An ANTAR domain dimer must contact each hexaloop of the dual hexaloop motif individually to prevent termination in eubacteria. Our findings thereby redefine the minimal ANTAR domain binding motif to a single hexaloop and revise the current model for ANTAR-mediated antitermination. These insights will inform and facilitate the discovery of novel ANTAR domain RNA targets.

Diversity and prevalence of ANTAR RNAs across actinobacteria

Background

Computational approaches are often used to predict regulatory RNAs in bacteria, but their success is limited to RNAs that are highly conserved across phyla, in sequence and structure. The ANTAR regulatory system consists of a family of RNAs (the ANTAR-target RNAs) that selectively recruit ANTAR proteins. This protein-RNA complex together regulates genes at the level of translation or transcriptional elongation. Despite the widespread distribution of ANTAR proteins in bacteria, their target RNAs haven’t been identified in certain bacterial phyla such as actinobacteria.

Results

Here, by using a computational search model that is tuned to actinobacterial genomes, we comprehensively identify ANTAR-target RNAs in actinobacteria. These RNA motifs lie in select transcripts, often overlapping with the ribosome binding site or start codon, to regulate translation. Transcripts harboring ANTAR-target RNAs majorly encode proteins involved in the transport and metabolism of cellular metabolites like sugars, amino acids and ions; or encode transcription factors that in turn regulate diverse genes.

Conclusion

In this report, we substantially diversify and expand the family of ANTAR RNAs across bacteria. These findings now provide a starting point to investigate the actinobacterial processes that are regulated by ANTAR.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02234-x.

Recent Advances in Genetic Tools for Acinetobacter baumannii

Acinetobacter baumannii is classified as a top priority pathogen by the World Health Organization (WHO) because of its widespread resistance to all classes of antibiotics. This makes the need for understanding the mechanisms of resistance and virulence critical. Therefore, tools that allow genetic manipulations are vital to unravel the mechanisms of multidrug resistance (MDR) and virulence in A. baumannii. A host of current strategies are available for genetic manipulations of A. baumannii laboratory-strains, including ATCC® 17978TM and ATCC® 19606T, but depending on susceptibility profiles, these strategies may not be sufficient when targeting strains newly obtained from clinic, primarily due to the latter's high resistance to antibiotics that are commonly used for selection during genetic manipulations. This review highlights the most recent methods for genetic manipulation of A. baumannii including CRISPR based approaches, transposon mutagenesis, homologous recombination strategies, reporter systems and complementation techniques with the spotlight on those that can be applied to MDR clinical isolates.