Photobacterium profundum
Encyclopedia
Photobacterium profundum is a deep sea Gammaproteobacterium, belonging to the family Vibrionaceae
and genus Photobacterium
. Like other members of this genus, P. profundum is a marine organism and has two circular chromosomes. P. profundum is a gram-negative
rod with the ability for growth at temperatures from 0 °C to 25 °C and pressures from 0.1 MPa to 70 MPa depending on the strain. It has a requirement for salt, is able to metabolise a wide range of simple and complex carbohydrates and has two flagella systems. Cells are rod shape, 2-4μm long and 0.8-1.0μm wide, with a single unsheathed flagella. This bacterium was originally isolated in 1986 from the Sulu Sea
and there are currently 4 cultured wild-type strains of P. profundum, (strains SS9, 3TCK, DJS4 and 1230).
P. profundum strain SS9 has optimal growth at 15 °C and 28 MPa making it both a psychrophile
and a piezophile
. P. profundum strain 3TCK, isolates from San Diego Bay
, grows optimally at 9 °C and 0.1 MPa and P. profundum strain DSJ4, isolated from the Ryukya trench off of Japan
at a depth of 5110 m, grows optimally at 10 °C and 10 MPa. Based on 16S rRNA sequence P. profundum is closely related to the Vibrio
genus, the most prominent species being the human pathogen Vibrio cholerae
.
In strain SS9 it has been shown that several stress response genes are up regulated in response to atmospheric pressure, these include htpG, dnaK, dnaJ, and groEL. The types and abundance of fatty acid chains in the cell membrane also respond to changes in pressure and temperature. At low temperature and high pressure strain SS9 increases the abundance of mono- and polyunsaturated fatty acids. This has the effect of increasing membrane fluidity by reducing packing of the fatty acid chains which results in a liquid crystal structure in the membrane rather than a gel structure. The outer membrane protein OmpH has been shown to be up regulated at elevated pressures, the opposite is true for the outer membrane protein OmpL which is up regulated in response to low pressures.
In 2005 Vezzi et al. published the genome sequence for P. profundum strain SS9. The genome of P. profundum consists of a 4.1-Mbp circular chromosome, a 2.2-Mbp minor circular chromosome, as well as a 80-kbp circular plasmid
. Strain SS9 has 14 ribosomal RNA (rRNA) genes on chromosome 1, and 1 on chromosome 2; this is the largest number of rRNA genes found in any bacterium. Chromosome 1 consists largely of genes which are essential for growth where as chromosome 2 appears to be a large plasmid, which, on an evolutionary time scale, has be gained several transposable elements. With in the genome of P. profundum there is a large number of open reading frames (ORF) which are unique to SS9 and not found in other members of the Vibrionaceae family.
The genome sequence also highlighted a full Stickland pathway for the fermentation of amino acids; this was the first time this pathway has been identified in an aerobic
bacterium. Two complete F1F0 ATP synthase pathways (one on each Chromosome) are also present in this bacterium: this might explain its ability to produce ATP
at both high and low pressure.
This work was followed by another paper in 2005 by Campanaro et al. which detailed microarray
work comparing gene expression at sub-optimal, optimal and supra-optimal temperatures and pressure for strains SS9, 3TCK and DSJ4. Campanaro et al. showed that there are 544 ORF’s divergent or missing from the 3TCK genome and 562 ORF’s divergent or missing from the DSJ4 chromosomes when compared to that of SS9. This paper also highlighted that 3TCK lacks the lateral flagella system which is up regulated in SS9 at elevated pressure as well as the absence of 3 phage-related regions from 3TCK and 4 phage-related regions from DSJ4.
Vibrionaceae
The Vibrionaceae are a family of Proteobacteria, given their own order. Inhabitants of fresh or salt water, several species are pathogenic, including the type species Vibrio cholerae, which is the agent responsible for cholera...
and genus Photobacterium
Photobacterium
Photobacterium is a genus of gram-negative bacteria in the family Vibrionaceae. Members of the genus are bioluminescent, that is they have the ability to emit light....
. Like other members of this genus, P. profundum is a marine organism and has two circular chromosomes. P. profundum is a gram-negative
Gram-negative
Gram-negative bacteria are bacteria that do not retain crystal violet dye in the Gram staining protocol. In a Gram stain test, a counterstain is added after the crystal violet, coloring all Gram-negative bacteria with a red or pink color...
rod with the ability for growth at temperatures from 0 °C to 25 °C and pressures from 0.1 MPa to 70 MPa depending on the strain. It has a requirement for salt, is able to metabolise a wide range of simple and complex carbohydrates and has two flagella systems. Cells are rod shape, 2-4μm long and 0.8-1.0μm wide, with a single unsheathed flagella. This bacterium was originally isolated in 1986 from the Sulu Sea
Sulu Sea
The Sulu Sea is a body of water in the southwestern area of the Philippines, separated from the South China Sea in the northwest by Palawan and from the Celebes Sea in the southeast by the Sulu Archipelago. Borneo is found to the southwest and Visayas to the northeast.Sulu Sea contains a number of...
and there are currently 4 cultured wild-type strains of P. profundum, (strains SS9, 3TCK, DJS4 and 1230).
P. profundum strain SS9 has optimal growth at 15 °C and 28 MPa making it both a psychrophile
Psychrophile
Psychrophiles or cryophiles are extremophilic organisms that are capable of growth and reproduction in cold temperatures, ranging from −15°C to +10°C. Temperatures as low as −15°C are found in pockets of very salty water surrounded by sea ice. They can be contrasted with thermophiles, which...
and a piezophile
Piezophile
A piezophile is an organism which thrives at high pressures, such as deep sea bacteria or archaea. They are generally found on ocean floors, where pressure often exceeds 380 atm . Some have been found at the bottom of the Pacific Ocean where the maximum pressure is roughly 117 MPa...
. P. profundum strain 3TCK, isolates from San Diego Bay
San Diego Bay
San Diego Bay is a natural harbor and deepwater port adjacent to San Diego, California. It is 12 mi/19 km long, 1 mi/1.6 km–3 mi/4.8 km wide...
, grows optimally at 9 °C and 0.1 MPa and P. profundum strain DSJ4, isolated from the Ryukya trench off of Japan
Japan
Japan is an island nation in East Asia. Located in the Pacific Ocean, it lies to the east of the Sea of Japan, China, North Korea, South Korea and Russia, stretching from the Sea of Okhotsk in the north to the East China Sea and Taiwan in the south...
at a depth of 5110 m, grows optimally at 10 °C and 10 MPa. Based on 16S rRNA sequence P. profundum is closely related to the Vibrio
Vibrio
Vibrio is a genus of Gram-negative bacteria possessing a curved rod shape, several species of which can cause foodborne infection, usually associated with eating undercooked seafood. Typically found in saltwater, Vibrio are facultative anaerobes that test positive for oxidase and do not form...
genus, the most prominent species being the human pathogen Vibrio cholerae
Vibrio cholerae
Vibrio cholerae is a Gram-negative, comma-shaped bacterium. Some strains of V. cholerae cause the disease cholera. V. cholerae is facultatively anaerobic and has a flagella at one cell pole. V...
.
In strain SS9 it has been shown that several stress response genes are up regulated in response to atmospheric pressure, these include htpG, dnaK, dnaJ, and groEL. The types and abundance of fatty acid chains in the cell membrane also respond to changes in pressure and temperature. At low temperature and high pressure strain SS9 increases the abundance of mono- and polyunsaturated fatty acids. This has the effect of increasing membrane fluidity by reducing packing of the fatty acid chains which results in a liquid crystal structure in the membrane rather than a gel structure. The outer membrane protein OmpH has been shown to be up regulated at elevated pressures, the opposite is true for the outer membrane protein OmpL which is up regulated in response to low pressures.
In 2005 Vezzi et al. published the genome sequence for P. profundum strain SS9. The genome of P. profundum consists of a 4.1-Mbp circular chromosome, a 2.2-Mbp minor circular chromosome, as well as a 80-kbp circular plasmid
Plasmid
In microbiology and genetics, a plasmid is a DNA molecule that is separate from, and can replicate independently of, the chromosomal DNA. They are double-stranded and, in many cases, circular...
. Strain SS9 has 14 ribosomal RNA (rRNA) genes on chromosome 1, and 1 on chromosome 2; this is the largest number of rRNA genes found in any bacterium. Chromosome 1 consists largely of genes which are essential for growth where as chromosome 2 appears to be a large plasmid, which, on an evolutionary time scale, has be gained several transposable elements. With in the genome of P. profundum there is a large number of open reading frames (ORF) which are unique to SS9 and not found in other members of the Vibrionaceae family.
The genome sequence also highlighted a full Stickland pathway for the fermentation of amino acids; this was the first time this pathway has been identified in an aerobic
Aerobic organism
An aerobic organism or aerobe is an organism that can survive and grow in an oxygenated environment.Faculitative anaerobes grow and survive in an oxygenated environment and so do aerotolerant anaerobes.-Glucose:...
bacterium. Two complete F1F0 ATP synthase pathways (one on each Chromosome) are also present in this bacterium: this might explain its ability to produce ATP
Adenosine triphosphate
Adenosine-5'-triphosphate is a multifunctional nucleoside triphosphate used in cells as a coenzyme. It is often called the "molecular unit of currency" of intracellular energy transfer. ATP transports chemical energy within cells for metabolism...
at both high and low pressure.
This work was followed by another paper in 2005 by Campanaro et al. which detailed microarray
Microarray
A microarray is a multiplex lab-on-a-chip. It is a 2D array on a solid substrate that assays large amounts of biological material using high-throughput screening methods.Types of microarrays include:...
work comparing gene expression at sub-optimal, optimal and supra-optimal temperatures and pressure for strains SS9, 3TCK and DSJ4. Campanaro et al. showed that there are 544 ORF’s divergent or missing from the 3TCK genome and 562 ORF’s divergent or missing from the DSJ4 chromosomes when compared to that of SS9. This paper also highlighted that 3TCK lacks the lateral flagella system which is up regulated in SS9 at elevated pressure as well as the absence of 3 phage-related regions from 3TCK and 4 phage-related regions from DSJ4.