The Draft Genome of Planococcus donghaensis MPA1U2 Reveals Nonsporulation Pathways Controlled by a Conserved Spo0A Regulon

Abstract

The Planococcaceae are extreme survivors, having been cultured from environments such as deep sea sediments, marine solar salterns, glaciers, permafrost, Antarctic deserts, and sea ice brine. The family contains both sporulating and nonsporulating genera. Here we present the unclosed, draft genome sequence of Planococcus donghaensis strain MPA1U2, a nonsporulating psychrotrophic bacterium isolated from surface coastal water of the Pacific Ocean.

GENOME ANNOUNCEMENT

Sporulation is an ancestral trait in the phylum Firmicutes. After several thousand years, however, DNA damage reaches irreparable levels in dormant spores (1). Some of the environments where Planococcus species have been isolated, such as the dry valleys of Antarctica, have a relative humidity below 10% and strong solar radiation (3), requiring active repair of DNA damage to survive (2). Because of this, the loss of sporulation in Planococcus may be an adaptation to persistent stress conditions.

Planococcus donghaensis strain MPA1U2 was isolated from cold surface coastal water of the Pacific Ocean near Santa Cruz, CA (+37°0′12.32″N, −122°11′9.51″W). The uncompleted draft genome has 3,307,315 bases and is comprised of 3,270 predicted open reading frames with a GC content of 39.7%. The frequency of individual reads is consistent with the presence of 5 to 6 copies of genes for 5S, 16S, and 23S rRNA. DNA sequencing was conducted by the UCSC Genome Sequencing Center using 454 GS FLX Titanium sequencing with 24× coverage. A draft, unclosed genome consisting of 74 contigs was obtained using Newbler. The genome was annotated using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP).

There are putative genes for complete tricarboxylic acid, glycolysis, and pentose phosphate pathways. Genes for starch and sucrose metabolism are present. Genes for carotenoid synthesis are arranged in an operon. There are also putative genes for the synthesis of all essential amino acids and a number of essential vitamins, including riboflavin, folate, and thiamine. There are no predicted phage-related sequences, transposons, insertion elements, extrachromosomal elements, or pseudogenes.

Although organisms in this genus do not form spores, P. donghaensis has several genes which regulate the initiation of sporulation in Bacillus subtilis. These include the following: the master regulator of sporulation, Spo0A; Spo0F, which receives phosphate from kinases; Spo0B, which transfers phosphate from Spo0F to Spo0A; and several histidine kinase A homologs. Phosphorylated Spo0A plays two roles in spore-forming species. The first role is to repress transcription of the transition state activator abrB, and the second is to activate expression of sporulation genes. The DNA motif recognized by Spo0A in the B. subtilis abrB promoter (4) was also found in the promoter of the abrB homolog in P. donghaensis, indicating that abrB repression is a conserved function. The consensus Spo0A binding motif also occurs in the promoter of the ppGpp synthetase RelA, suggesting that the sporulation module has been conserved for its independent stress-integrating capacity, and that this function has become integrated with the stringent response.

Planococcus donghaensis is an example of an organism in which sporulation was eliminated because it did not provide a viable alternative to efficient persistence in extremely tough environments. The Planococcaceae family contains independent examples of sporulation loss along the branches leading to Filibacter, Caryophanon, Kurthia, and Planomicrobium/Planococcus (5). Further investigations into this family of bacteria may help unravel the complex sporulation pathway from other mechanisms of stress resistance.

Nucleotide sequence accession numbers.

This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under accession number AEPB00000000. The version described in this paper is the first version, AEPB01000000.