Comparative transcriptome analysis reveals different adaptation mechanisms for degradation of very long-chain and normal long-chain alkanes in Dietzia sp. DQ12-45-1b.

Hydrocarbon-degrading bacteria typically metabolize a broad range of alkane substrates, but global metabolic characteristics of strains growing on alkane substrates in different chain lengths remain unclear. In this study, we analysed the transcriptional profiles of a hydrocarbon degrading bacterium, Dietzia sp. DQ12-45-1b, during growth on octacosane (C28), hexadecane (C16) and glucose as the sole carbon sources. Our results highlight that C16 and C28 induced common genes of core alkane degradation pathways in DQ12-45-1b, whereas transcriptional patterns of genes related to lipid metabolism, energy metabolism, biomass synthesis, and metal ion transportation were distinct. In addition, the transcriptional differences of genes related to glyoxylate shunt (GS) as well as growth phenotypes of mutant strain with defects in GS demonstrated that GS is essential for C16 degradation, though it is dispensable for C28 degradation in DQ12-45-1b. These results demonstrate that DQ12-45-1b cells exhibited considerable metabolic flexibility by using various mechanisms during growth on alkane substrates in different chain lengths. This study advances our knowledge of microbial hydrocarbon degradation and provides valuable information for the application of alkane-degrading bacteria in bioremediation and microbial enhanced oil recovery.

Single-Homology-Arm Linear DNA Recombination by the Nonhomologous End Joining Pathway as a Novel and Simple Gene Inactivation Method: a Proof-of-Concept Study in Dietzia sp. Strain DQ12-45-1b.

Nonhomologous end joining (NHEJ) is critical for genome stability because of its roles in double-strand break repair. Ku and ligase D (LigD) are the crucial proteins in this process, and strains expressing Ku and LigD can cyclize linear DNA in vivo Here, we established a proof-of-concept single-homology-arm linear DNA recombination for gene inactivation or genome editing by which cyclization of linear DNA in vivo by NHEJ could be used to generate nonreplicable circular DNA and could allow allelic exchanges between the circular DNA and the chromosome. We achieved this approach in Dietzia sp. strain DQ12-45-1b, which expresses Ku and LigD homologs and presents NHEJ activity. By transforming the strain with a linear DNA single homolog to the sequence in the chromosome, we mutated the genome. This method did not require the screening of suitable plasmids and was easy and time-effective. Bioinformatic analysis showed that more than 20% of prokaryotic organisms contain Ku and LigD, suggesting the wide distribution of NHEJ activities. Moreover, an Escherichia coli strain also showed NHEJ activity when the Ku and LigD of Dietzia sp. DQ12-45-1b were introduced and expressed in it. Therefore, this method may be a widely applicable genome editing tool for diverse prokaryotic organisms, especially for nonmodel microorganisms.IMPORTANCE Many nonmodel Gram-positive bacteria lack efficient genetic manipulation systems, but they express genes encoding Ku and LigD. The NHEJ pathway in Dietzia sp. DQ12-45-1b was evaluated and was used to successfully knock out 11 genes in the genome. Since bioinformatic studies revealed that the putative genes encoding Ku and LigD ubiquitously exist in phylogenetically diverse bacteria and archaea, the single-homology-arm linear DNA recombination by the NHEJ pathway could be a potentially applicable genetic manipulation method for diverse nonmodel prokaryotic organisms.

Dopamine D2 receptor gene polymorphisms in newborn infants of drug-using women.

OBJECTIVES: To determine the characteristics of dopamine D2 receptor gene (DRD2) polymorphisms in drug-exposed and unexposed neonates and the relationship to neonatal abstinence syndrome (NAS). DESIGN: Retrospective case-control analysis between drug-exposed and unexposed infants between DRD2 polymorphisms, drug exposure and NAS treatment. PATIENTS: Drug-exposed (n=48) and drug-free (n=49) infants born between March 1999 and December 2006. METHODS: Analysis of DNA for the Taq1A, -141Ins/Del and Ser311Cys DRD2 polymorphisms. Drug exposure was determined by antenatal maternal drug and alcohol history. Frequency measures of DRD2 polymorphisms were compared between drug-exposed infants, treatment NAS medication and with control infants. SETTING: Tertiary maternity hospital, Sydney, Australia. MAIN OUTCOME MEASURES: All infants were born in a good condition (25.7% <37 weeks gestation). Opiates (methadone and heroin) were used by 45 (93.8%) of drug-exposed mothers. The A2A2 allele was more common in drug-exposed infants (37 (77.0%) versus 23 (46.9%), p=0.003) but the A1A2 allele was more common in control infants (23 (46.9%) versus 4 (8.3%), p=0.00002). The-ins allele was more common in control (39 (79.6%) versus 20 (41.7%), p=<0.01) and unmedicated drug-exposed (14/25 (56%) versus 5/23 (21.7%), p=0.02) infants. The majority of infants (41 (83.7%) controls versus 41 (85.4%), p=1.000) expressed the least common, Ser polymorphism. CONCLUSIONS: DRD2 polymorphisms are detectable from DNA obtained from stored blood spots. The -ins allele is more common in control and unmedicated drug-exposed infants. Further study is recommended to explore postneonatal outcomes especially in relation to neuropsychiatric behaviours.