Oceanobacillus iheyensis

A Microbial Biorealm page on the genus Oceanobacillus iheyensis

Classification

Higher order taxa

Bacteria; Firmicutes; Bacillales; Oceanobacillus

Species

iheyensis HTE831

Genus species Oceanobacillus iheyensis HTE831

Description and significance

Oceanobacillus iheyensis HTE831 is an extremely halotolerant and alkaliphilic Bacillus related species. It is isolated from deep sea sediment collected at a depth of 1050m on the Iheya Ridge.(1) The strain is aerobic, Gram positive, rod-shaped, and spore forming. It is motile by the use of meretricious flagella. Isolate HTE831 grows from a pH range of 6.5-9.5 and in 0-21% NaCl. The salinities were 0-21% in NaCl at pH 7.5 and 0-18% NaCl at pH 9.5. The proposal that O.iheyensis is a member of a new species in a new genus came after phylogenetic analysis using 16S rDNA sequencing, chemotaxonomy, and the physiology of strain HTE831. (1)

Genome structure

The genome of O.iheyensis is a single circular chromosome consisting of 3,630,528 nt. The entire genome sequence for O.iheyensis has been determined in Japan MSTC sequencing center. There are 3594 genes and 3500 are protein coding with 92 structural RNAs. The genome has 3496 ORFs with 1972 assigned functions. (1) Six new kind of insertion sequences (Iss), IS667 to IS672, a group II intron (Oi.Int), and an incomplete transponson (Tn8521oi) were identified in O.iheyensis. All the new insertion sequences except IS699 made a 4 to 8 bp duplication of the target site sequence. (5) The ISs carried 23 to 28 bp inverted repeats. Most of the ISs and the group II intron are widely distributed throughout the genome and were inserted in noncoding regions. In HTE831 genome there are 19 identified ISs. Seven of these were truncated, showing the occurrence of internal genome rearrangement. (5)

Cell structure and metabolism

The gram positive bacteria have a thick peptidoglycan cell wall as its outmost layer. This layer is covered all over with flagella (peritrichous) that is used for motility. The flagella are inserted through the cell wall in a multi-step process. The cell wall protects the cell membrane made up of a lipid bilayer. The plasma membrane encloses the nucleoid, inclusion bodies and other cytoplasmic proteins. HTE831 is a bacillus which means it is rod shaped. Oceanobacillus iheyensis can change its phenotype and become a spore. It then has a core, plasma membrane, germ cell wall, cortex, inner spore coat and the outer spore coat cover enclosed in the exosprorium. The cell wall is very important in alkaliphilic Bacillus species because their protoplasts can lose stability in alkaline environments. The species contain certain acid polymers; galacturonic acid, gluconic acid, glutamate, aspartate and phosphoric acid. This allows the pH values inside the polymer layer (cell wall) to be more acidic that the surrounding environment. (2) Akira Funahashi received the B.E., M.E. and Ph.D. degrees from Keio University, Japan found close to 100 metabolistic functions of O.inheyensis. They include; glycolysis / gluconeogenesis, TCA cycle, PPP, Fructose and mannose metabolism, Urea cycle and metabolism of amino groups, glutamate metabolism, penicillins and cephalosporins biosynthesis, D-arginine and D-ornithine metabolism, Petidoglycan biosynthesis, Pyruvate metabolism, Carbon fixation, CO2 fixation, Nitrogen and Sulfer metabolism, plus many others. (7) O.iheyensis gains its energy through numerous metabolic pathways such as glycolysis, starch and sucrose metabolism, galactose metabolism and carbon fixation. [view in KEGG](7) Along with metabolism this organism must also maintain intracellular homeostasis. In aerobic bacteria, various antiport and symport systems are used. The H+/Na+ symporter uses the dicarboxylate transport carriers to catalyze the up take of C4-dicarboxylates. This plays an important role in aerobic alkaliphilic species for pH homeostasis.(2)

Ecology

In nature, bacillus species are distributed nearly ubiquitously. Microbial populations are influenced by the nature of the chemical and physical environment in which they grow. Stable or stressful conditions can have the bacteria interact with other microbes in the immediate environment. The deep sea is principally a cold, dark, oligotrophic, and high pressure environment. However, even in this environment the bottom of the sea is not devoid of organisms.(8) The deep sea sediment consists of various extremophilic bacteria such as alkaliphiles, thermopiles, and psychrophiles. It is also composed of actinomycetes, fungi, and non-extromophilic bacteria.(1,8) Important aspects of O.iheyensis involvement in its natural habitat includes it ability to produce antibiotics([view in KEGG]) to keep its ecological niche, to undergo sporulation in diverse conditions, and the vast quantities of proteins and enzymes that O.iheyensis produces.(7)

Pathology

Oceanobacillus iheyensis generally have no contact with humans and cause no disease. It is a free living, aerobic strain that is organic. www.ncbI.nlm.nih.gov/entrez/query

Application to Biotechnology

O.iheyensis and other extremophilic microorganisms are already used for some biotechnological processes. The production of bacteriohodopsin is from the use of halobateria.(9) There are several other potential and present applications being reviewed; the production of polymers (I.E. polysaccharides), enzymes, and compatible solutes, and the use of these extremophiles in enhanced oil recovery, cancer detection, drug screening and the biodegradation of residues and toxic compounds.(9) O. iheyensis has at least 29 'proteolytic' enzymes, which could be important in future industrial applications or can be used as additives in laundry detergent.(10) The use of Chaperone protein htpG (Heat shock protein htpG) (High temperature protein G), 33 kDa chaperonin (Heat shock protein 33 homolog) (HSP33),or Heat-inducible transcription repressor hrcA could allow for laundry detergent to become or remain active in high temperatures.(12) A final application is O.iheyensis ability to produce antibiotics. O.iheyensis can make inhibitors of pantothenate kinase which is needed for organisms like Staphylococcus aureus to make coenzyme A. Coenzyme A (CoA) is an essential cofactor for maintaining the organisms life.(11)

Current Research

Proteomics one of the latest techniques in evaluating organisms was completed on Oceanobacillus iheyensis. Dr. Robert Graham performed the first multidimensional analysis of the insoluble sub proteome of the halo tolerant deep-sea bacterium O.iheyensis HTE 831. (14) Proteome; “The term has been applied to several different types of biological systems. A cellular proteome is the collection of proteins found in a particular cell type under a particular set of environmental conditions such as exposure to hormone stimulation. It can also be useful to consider an organism's complete proteome, which can be conceptualized as the complete set of proteins from all of the various cellular proteomes. This is very roughly the protein equivalent of the genome.” (Wikipedia) A total of 4352 peptides were initially identified by using a multidimensional gel-based and gel-free analysis. The subsequent peptide list was reduced to 467 using PROVALT. Theses peptides were unique and resulted in the positive identification of 153 proteins.(15) Functions were assigned to a large number of the proteins and 41 proteins were predicted to have signal peptides. The analysis also allowed the identification of two putative transport systems believed important in O.iheneysis HTE831 alkaliphilic adaptation.(15)In FEMS Microbiology Review the molecular insights into the initiation of sporulation in Gram-positive bacteria was surveyed using new technologies. Changes in scientific technologies over the last decade has significantly impacted the study of life sciences. Because of new technologies the study of the master regulator of sporulation, Spo0A, in low G+C Gram-positive endospore-forming bacteria was able to be reviewed from the genome sequence data.(16)Genome sequence of Oceanobacillus iheyensis showed unexpected adaptive capabilities to extreme environments. The bacterium habitat is in the deep sea sediment, therefore it is extremely halotolerant and alkaliphilic. The genome sequence was presented along with analysis of the genes required for theadaptation of the extreme habitant environment. The alkaliphilic genes were determined based on comparative analysis with other Bacillus species. These comparison brought useful understanding in the life of highly alkaline environments and microbial diversity.

References

(1)Oceanobacillus iheyensis gen. nov., sp. nov., a deep-sea extremely halotolerant and alkaliphilic species isolated from a depth of 1050 m on the Iheya Ridge.Lu J, Nogi Y, Takami H.Microbial Genome Research Group, DEEPSTAR, Japan Marine Science and Technology Center, 2-15 Natsushima, 237-0061, Yokosuka, Japan.

(2)Hideto Takami,a Yoshihiro Takaki, and Ikuo Uchiyama1 Japan Marine Science and Technology Center, Microbial Genome Research Group, 2–15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan and 1Research Center for Computational Science, Okazaki National Research Institute, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-85

(3)Takami H., Inoue,A., Fuji,F. and Horikoshi,K. (1997) Microbial flora in the deepest sea mud of Mariana Trench. FEMS Microbiol. Lett., 152:, 279–285. [PubMed].

(4)Takami H., Kobata,K., Nagahama,T., Kobayashi,H., Inoue,A. and Horikoshi,K. (1999) Biodiversity in deep-sea sites near the south part of Japan. Extremophiles, 3:, 97–102. [PubMed].

(5)Priest F.G. (1993) Systematics and ecology of Bacillus. In Sonenshein,A.L., Hoch,J.A. and Losick,R. (eds), Bacillus subtilis and Other Gram-Positive Bacteria. ASM Press, Washington, DC, pp. 3–16.

(6)Takami H. (1999) Isolation and characterization of microorganisms from deep-sea mud. In Horikoshi,K. and Tsujii,K. (eds), Extremophiles in Deep-Sea Environments. Springer-Verlag, Tokyo, Japan, pp. 3–26.

(7) Akira Funahashi<funa@symbio.jst.go.jp> Wed Jun 16 22:52:26 JST 2004Oceanobacillus iheyensis. Glycolysis / Gluconeogenesis, [SBML: Level-1 ver-2| Level-2 ver-1 ], [view in KEGG]. Citrate cycle (TCA cycle), [SBML: Level-1 ... sbserv.symbio.jst.go.jp/001/kegg/oih.html

(8) Deep-sea Microorganism Research Group, Japan Marine Science and Technology Center, Yokoruka, Japan. takamih@jamstec.go.jp

(9) Ventosa, A. and Nieto, J.J.: Biotechnological applications and potentialities of halophilic microorganisms. World J. Microbiol.Biotechnol., 11, 85-94 (1995).

(10)www.ebi.ac.uk/2can/genomes/bacteria/Oceanobacillus_iheyensis.html - 9k -

(11) Anthony E. Choudhry,1 Tracy L. Mandichak,1† John P. Broskey,1 Richard W. Egolf,1† Cynthia Kinsland,2 Tadhg P. Begley,2 Mark A. Seefeld,1 Thomas W. Ku,1,James R. Brown,1* Magdalena Zalacain,1 and Kapila Ratnam1*Microbial, Musculoskeletal and Proliferative Diseases and Bioinformatics, GlaxoSmithKline Pharmaceuticals, Collegeville, Pennsylvania 19426,1 and Department of Chemistry and Chemical Biology, Cornell University, Ithaca New York 148502 Received 22 November 2002/Returned for modification 20 January 2003/Accepted 28 February 2003

(12) 625 Oceanobacillus iheyensis PIRSF002583 300 PubMed ID=>12235376

(13)Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments. [Nucleic Acids Res. 2002] PMID: 12235376

(14)Robert L. J. Graham, Catherine E. Pollock, S. Naomi O'Loughlin, Nigel G. Ternan, D. Brent Weatherly, Rick L. Tarleton, Geoff McMullan. (2007) Multidimensional analysis of the insoluble sub-proteome ofOceanobacillus iheyensis HTE831, an alkaliphilic and halotolerant deep-sea bacterium isolated from the Iheya ridge. PROTEOMICS 7:1, 82

Edited by student Gloria Slusher