Summary: Actinobacteria constitute one of the largest phyla among Bacteria and represent gram-positive bacteria with a high G+C content in their DNA. This bacterial group includes microorganisms exhibiting a wide spectrum of morphologies, from coccoid to fragmenting hyphal forms, as well as possessing highly variable physiological and metabolic properties. Furthermore, Actinobacteria members have adopted different lifestyles, and can be pathogens (e.g., Corynebacterium, Mycobacterium, Nocardia, Tropheryma, and Propionibacterium), soil inhabitants (Streptomyces), plant commensals (Leifsonia), or gastrointestinal commensals (Bifidobacterium). The divergence of Actinobacteria from other bacteria is ancient, making it impossible to identify the phylogenetically closest bacterial group to Actinobacteria. Genome sequence analysis has revolutionized every aspect of bacterial biology by enhancing the understanding of the genetics, physiology, and evolutionary development of bacteria. Various actinobacterial genomes have been sequenced, revealing a wide genomic heterogeneity probably as a reflection of their biodiversity. This review provides an account of the recent explosion of actinobacterial genomics data and an attempt to place this in a biological and evolutionary context.

Genomics of Actinobacteria: Tracing the Evolutionary History of an Ancient Phylum

Although microorganisms are extremely good in presenting us with an amazing array of valuable products, they usually produce them only in amounts that they need for their own benefit; thus, they tend not to overproduce their metabolites. In strain improvement programs, a strain producing a high titer is usually the desired goal. Genetics has had a long history of contributing to the production of microbial products. The tremendous increases in fermentation productivity and the resulting decreases in costs have come about mainly by mutagenesis and screening/selection for higher producing microbial strains and the application of recombinant DNA technology.

Genetic improvement of processes yielding microbial products

Antibiotic resistance genes have become highly mobile since the development of antibiotic chemotherapy. A considerable body of evidence exists proving the link between antibiotic use and the significant increase in drug-resistant human bacterial pathogens. The application of molecular detection and tracking techniques in microbial ecological studies has allowed the reservoirs of antibiotic resistance genes to be investigated. It is clear that the transfer of resistance genes has occurred on a global scale and in all natural environments. The considerable diversity of bacteria and mobile elements in soils has meant that the spread of resistance genes has occurred by all currently known mechanisms for bacterial gene transfer. Trans-kingdom transfers from plants to bacteria may occur in soil. Hot spots for gene transfer in the soil/plant environment have been described and colonized niches such as the rhizosphere and other nutrient-enriched sites, for example manured soil, have been identified as reservoirs of resistance genes. Although exposure and selection for tolerance of antibiotics is considerable in clinical environments there is increasing evidence that selection for resistant phenotypes is occurring in natural environments. Antibiotic-producing bacteria are abundant in soil and there is evidence that they are actively producing antibiotics in nutrient-enriched environments in soil. In addition there is clear evidence that the self-resistance genes found within antibiotic gene clusters of the producers have transferred to other non-producing bacteria. Perhaps most important of all is the use of antibiotics in agriculture as growth promotants and for treatment of disease in intensively reared farm animals. These treatments have resulted in gut commensal and pathogenic bacteria acquiring resistance genes under selection and then, due to the way in which farm slurries are disposed of, the spread of these genes to the soil bacterial community. Integrons with multiple resistance gene cassettes have been selected and disseminated in this way; many of these cassettes carry other genes such as those conferring heavy metal and disinfectant resistance which have been co-selected in bacteria surviving in effluents and contaminated soils, further maintaining and spreading the antibiotic resistance genes.

Occurrence and reservoirs of antibiotic resistance genes in the environment

Physical maps of the chromosomes of three strains of Streptomyces ambofaciens were constructed by ordering Asel fragments generated from the genomic DNA as a single linear chromosome of about 8 Mb. The physical maps of the three strains were very similar. For strain DSM40697, a Dral map was obtained by positioning the Dral sites relative to the Asel map. Eighteen genetic markers as well as the deletable and amplifiable region were assigned to the Asel and Dral fragments in this strain. The resulting genetic map resembled that of Streptomyces coelicolor A3(2). The two terminal Asel fragments exhibited retarded pulsed-field gel electrophoresis mobility, demonstrating that proteins are covalently bound at this position. A restriction map of this region was made using four additional endonucleases. Repeated sequences present at both ends of the chromosome were mapped as long terminal inverted repeats stretching over 210 kb. This corresponds to the longest terminal inverted repeats so far characterized. The deletable region of S. ambofaciens was localized at the chromosomal extremities.

The unstable region of Streptomyces ambofaciens includes 210 kb terminal inverted repeats flanking the extremities of the linear chromosomal DNA.

https://www.cell.com/cell-chemical-biology/pdf/S1074-5521(05)00030-X.pdf

Cyclization Mechanism for the Synthesis of Macrocyclic Antibiotic Lankacidin in Streptomyces rochei

The linear plasmid pPZG101 of Streptomyces rimosus R6 was restriction mapped with the enzymes Asel, Bfrl, Dral and Xbal. It is 387 kb in size and the ends are inverted repeats of at least 95 kb in length. Twenty spontaneous morphological variants and seventeen auxotrophic mutants were screened for changes in the plasmid. Two strains were found that had lost all plasmid sequences. Four strains had integrated parts of the plasmid into the chromosome. Restriction analysis suggested that at least three of the integrated strains had retained free plasmid ends. If it is assumed that the chromosome of S. rimosus R6 is linear, this might be explained by replacement of one or both chromosome ends by a plasmid end. One strain, which overproduced oxytetracycline, carried an enlarged linear plasmid of 1 Mb in size that had acquired chromosomal sequences from the oxytetracycline biosynthesis cluster.

/pdf/the-387-kb-linear-plasmid-ppzg101-of-streptomyces-rimosus-5e8yts59g3.pdf

The 387 kb linear plasmid pPZG101 of Streptomyces rimosus and its interactions with the chromosome.

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The 387 kb linear plasmid pPZG101 of Streptomyces rimosus and its interactions with the chromosome.