Rubber Degrading Strains of Microtetraspora and Dactylosporangium

Latex clearing protein (lcp) found in Actinobacterial strains is reportedly critical for the initial oxidative cleavage of poly(cis-1,4-isoprene), the major polymeric unit of rubber. In this study, we screened 940 Actinobacterial strains isolated from various locations in Sarawak on NR latex agar and identified 18 strains from 5 genera that produced clearing zones and contained (latex clearing protein) lcp genes. We report here the first lcp genes from Microtetraspora sp. AC03309 (lcp 1 and lcp2) and Dactylosporangium sp. AC04546 (lcp1, lcp2, lcp3), together with their operon structure. Complete 16S rDNA gene sequence revealed that Dactylosporangium sp. AC04546 is 99% identical to Dactylosporangium sucinum RY35-23 whereas Microtetraspora sp. AC03309 is 98% identical to Microtetraspora glauca IFO14761. Morphological images and the spectrophotometric detection of aldehyde and keto groups in rubber samples incubated with the strains confirm the strains’ ability to degrade rubber-based products.

Noncontiguous operon is a genetic organization for coordinating bacterial gene expression

Bacterial genes are typically grouped into operons defined as clusters of adjacent genes encoding for proteins that fill related roles and are transcribed into a single polycistronic mRNA molecule. This simple organization provides an efficient mechanism to coordinate the expression of neighboring genes and is at the basis of gene regulation in bacteria. Here, we report the existence of a higher level of organization in operon structure that we named noncontiguous operon and consists in an operon containing a gene(s) that is transcribed in the opposite direction to the rest of the operon. This transcriptional architecture is exemplified by the genes menE-menC-MW1733-ytkD-MW1731 involved in menaquinone synthesis in the major human pathogen Staphylococcus aureus. We show that menE-menC-ytkD-MW1731 genes are transcribed as a single transcription unit, whereas the MW1733 gene, located between menC and ytkD, is transcribed in the opposite direction. This genomic organization generates overlapping transcripts whose expression is mutually regulated by transcriptional interference and RNase III processing at the overlapping region. In light of our results, the canonical view of operon structure should be revisited by including this operon arrangement in which cotranscription and overlapping transcription are combined to coordinate functionally related gene expression.

OperomeDB: A Database of Condition-Specific Transcription Units in Prokaryotic Genomes

Background. In prokaryotic organisms, a substantial fraction of adjacent genes are organized into operons—codirectionally organized genes in prokaryotic genomes with the presence of a common promoter and terminator. Although several available operon databases provide information with varying levels of reliability, very few resources provide experimentally supported results. Therefore, we believe that the biological community could benefit from having a new operon prediction database with operons predicted using next-generation RNA-seq datasets.Description. We present operomeDB, a database which provides an ensemble of all the predicted operons for bacterial genomes using available RNA-sequencing datasets across a wide range of experimental conditions. Although several studies have recently confirmed that prokaryotic operon structure is dynamic with significant alterations across environmental and experimental conditions, there are no comprehensive databases for studying such variations across prokaryotic transcriptomes. Currently our database contains nine bacterial organisms and 168 transcriptomes for which we predicted operons. User interface is simple and easy to use, in terms of visualization, downloading, and querying of data. In addition, because of its ability to load custom datasets, users can also compare their datasets with publicly available transcriptomic data of an organism.Conclusion. OperomeDB as a database should not only aid experimental groups working on transcriptome analysis of specific organisms but also enable studies related to computational and comparative operomics.