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The extensive environmental adaptability of the genus Paenibacillus is related to the enormous diversity of its gene repertoires. Paenibacillus sp. SSG-1 has previously been reported, and its agar-degradation trait has attracted our attention. Here, the genome sequence of Paenibacillus sp. SSG-1, together with 76 previously sequenced strains, was comparatively studied. The results show that the pan-genome of Paenibacillus is open and indicate that the current taxonomy of this genus is incorrect. The incessant flux of gene repertoires resulting from the processes of gain and loss largely contributed to the difference in genomic content and genome size in Paenibacillus. Furthermore, a large number of genes gained are associated with carbohydrate transport and metabolism. It indicates that the evolution of glycometabolism is a key factor for the environmental adaptability of Paenibacillus species. Interestingly, through horizontal gene transfer, Paenibacillus sp. SSG-1 acquired an approximately 150 kb DNA fragment and shows an agar-degrading characteristic distinct from most other non-marine bacteria. This region may be transported in bacteria as a complete unit responsible for agar degradation. Taken together, these results provide insights into the evolutionary pattern of Paenibacillus and have implications for studies on the taxonomy and functional genomics of this genus.

Prototheca stagnorum belongs to the genus Prototheca that are achloroplyllous algae with phylogenetic affinities to Chlorella sp. Microalgae of the genus Prototheca spp are associated with rare algal infections of invertebrates termed protothecosis. In this study, the complete nucleotide sequence of the circular mitochondrial (mt) DNA of the chlorophyte alga P. stagnorum has been determined (80,023 base-pairs, A þ T content 13.77%). The genes identified encode three subunits of the cytochrome oxidase and apocytochrome b, eight subunits of the NADH dehydrogenase complex (nad1-7, nad4L), four ATPase subunits (atp1, atp4, atp6, atp8), three ribosomal RNAs (5 S (rrn5), small subunit (srn) and large subunit (lrn) RNA), 27 tRNAs, two succinate dehydrogenase and 10 ribosome proteins. The complete mitochondrial genome sequence will provide new molecular biology information to further understand the genetic diversity of the Prototheca sp. and to eliminate this population.

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Background Dunaliella salina is a high-quality industrial effector for carotenoid production. Although the accumulation of carotenoids in D. salina increases under red light conditions, the content of carotenoids in the algal cell decreases. The mechanism by which red light regulates carotenoid synthesis is still unclear.Results In this study, a transcription factor of DsGATA1 with a distinct structure was discovered in D. salina. The recognition motif of DsGATA1 was comparable to that of plant and fungal GATA, despite its evolutionary proximity to animal-derived GATA. The expression of DsGATA1 in D. salina was still noticeably decreased when exposed to red light. Analysis of physiological and biochemical transcriptomic data from overexpressed, interfering and wild-type strains of DsGATA1 revealed that DsGATA1 acts as a global regulator of D. salina carotenoid synthesis. The upregulated genes in the CBP pathway by DsGATA1 were involved in its regulation of the synthesis of carotenoids. DsGATA1 also enhanced carotenoid accumulation under red light by affecting N metabolism. DsGATA1 was found to directly bind to the promoter of nitrate reductase to activate its expression, promoting D. salina nitrate uptake and accelerating biomass accumulation. DsGATA1 affected the expression of the genes encoding GOGAT, GDH and ammonia transporter proteins. Moreover, our study revealed that the regulation of N metabolism by DsGATA1 led to the production of NO molecules that inhibited carotenoid synthesis. However, DsGATA1 significantly enhanced carotenoid synthesis by NO scavenger removal of NO. The D. salina carotenoid accumulation under red light was elevated by 46% in the presence of overexpression of DsGATA1 and NO scavengers.Conclusion It was found that a transcription factor of DsGATA1 from D. salina has a distinct structure and recognition motif. The novel gene encoding DsGATA1 enhanced the production of carotenoids under red light and endowed D. salina with high algal biomass. The regulation of terpenoid metabolism by DsGATA1 is different from that reported for GATA factors. DsGATA1 yet enhanced the production of NO in D. salina. Nevertheless, our results indicated that DsGATA1 could be an important target for engineering carotenoid production.