## 5 Advances in Systems Level Understanding of the CA Production in _S. clavuligerus_  
In the recent decade, whole system-level approaches and omics technologies are being developed to explore and understand the existing complex interaction between different biological layers, such as the genome, transcriptome, proteome, and metabolism. A deeper understanding of the BGCs regulation and expression in _S. clavuligerus_ is important to improve the CA production in submerged cultures. The first draft genome of _S. clavuligerus_ was sequenced by two independent research groups in 2010 [121; 122]. The genome is composed of a 6.8 Mb chromosome and four linear plasmids named pSCL1 (11 kb), pSCL2 (150 kb), pSCL3 (430 kb), and pSCL4 (1.8 Mb), and a GC% of 72. The global annotation of this genome refers six rRNA operons, 66 tRNA genes, and 7898 protein-coding genes (5700 in the chromosome). The _S. clavuligerus_ genome contains a plethora of BGCs that includes secondary metabolites like staurosporine, moonomycin, terpenes, pentalenenes, phytoenes, siderophores, lentibiotics, holomycin, cebphamycin C, and CA [121]. Specifically, the gene cluster of CA is situated in the chromosome and there exists a paralog gene cluster located in the pSCL4 plasmid codifying for CA and clavam metabolite production. In 2016, the genome of a _S. clavuligerus_ industrial strain (F613-1) was sequenced. The assembly of the genome sequences identified a chromosome and a plasmid. The main differences were reported in the plasmid of F613-1, which contains a smaller number of coding genes compared to the 1.8 Mb megaplasmid of _S. clavuligerus_ ATCC 27064 [123]. The significance of these differences needs further investigations. Recently, [PERSON] and colleagues [124] performed a complete systems biology analysis for identifying new regulatory elements and BGCs in _S. clavuligerus_ using new generation high-throughput technologies. In this research, the authors sequenced a high-quality genome of _S. clavuligerus_ ATCC 27064, and it was used as a template to integrate the ribosome profiling and differential RNA-seq data. In that study, 58 potential BGCs were identified, including CA, 5S clavams, holomycin, tunicamycin, and 14 terpene type and 12 polyketides type BGCs. Furthermore, 2659 Transcription Start Sites (TSSs) and regulatory elements in the whole genome were identified. The same study reported that COG functional categories like coenzymes, secondary metabolites, inorganic ions, carbohydrate, and amino acid metabolism exhibited high differential expression levels during distinct growth phases while categories like signal transduction, replication, and cell division exhibited constitutive expression during all growth phases. Similarly, [PERSON] and colleagues presented a high-quality genome and developed a data mining analysis for identifying secondary metabolite BGCs in thirty _Streptomyces_ strains, including improvements in previous genome annotations and the identification of 43 BGCs in _S. clavuligerus_[125]. Similar approaches were performed for other bacteria of the _Streptomyces_ genus [126]. Although the analysis and study of the transcriptome in _S. clavuligerus_ have been relevant for identifying regulatory elements in the genome, they are also useful for understanding the up- or downregulation of metabolic pathways involved in CA production at specific nutritional conditions. In 2011, [PERSON] et al. [118] developed the first comparative transcriptome analysis of a _S. clavuligerus_ industrial strain (engineered by random mutagenesis) versus a wild type strain. They captured transcript changes in central carbon and secondary metabolism, specifically, upregulation of ammonium and phosphate transporters, and glutamine and glutamate synthase genes. In 2014, [PERSON] and co-workers [127] developed a comparative transcriptomic analysis between a _caR_-deleted mutant and the wild type strain _S. clavuligerus_ ATCC 27064.