Computational genomics of photosynthetic organisms

Photosynthetic organisms

“Sunlight plays a much larger role in our sustenance than we may expect: all the food we eat and all the fossil fuel we use is a product of photosynthesis, which is the process that converts energy in sunlight to chemical forms of energy that can be used by biological systems. Photosynthesis is carried out by many different organisms, ranging from plants to bacteria. The best known form of photosynthesis is the one carried out by higher plants and algae, as well as by cyanobacteria and their relatives, which are responsible for a major part of photosynthesis in oceans. All these organisms convert CO2(carbon dioxide) to organic material by reducing this gas to carbohydrates in a rather complex set of reactions. Electrons for this reduction reaction ultimately come from water, which is then converted to oxygen and protons. Energy for this process is provided by light, which is absorbed by pigments (primarily chlorophylls and carotenoids). Chlorophylls absorb blue and red light and carotenoids absorb blue-green light, but green and yellow light are not effectively absorbed by photosynthetic pigments in plants; therefore, light of these colors is either reflected by leaves or passes through the leaves. This is why plants are green”

—Wim Vermaas [VERMAAS1998].

Each organism introduced in this section has different characteristics and behaviors that make interesting to analyze its genomic information [1].

[VERMAAS1998]Vermaas, Wim. “An Introduction to Photosynthesis and Its Applications.” The World & I Mar. 1998. 28 Nov. 2005 http://photoscience.la.asu.edu/photosyn/education/photointro.html.

Cyanobacteria

Cyanobacteria are the only prokaryotes that perform oxygenic photosynthesis. Cyanobacteria were formerly known as blue-green algae but this term has been abandoned when their prokaryotic nature became apparent [STANIER1962]. As a monophyletic group within the Kingdom Bacteria, cyanobacteria are remarkably diverse, both with respect to their morphology as well as to their physiology and metabolism.

Cyanobacteria combine the fixation of CO2 and N2, the two most important biogeochemical processes on Earth. They are globally important primary producers and contribute greatly to the global nitrogen budget [KARL2002].

Cyanobacteria are also exceptional because some representatives are capable of cell differentiation which is unique among prokaryotes. Many species reveal a remarkable flexibility and adapt to a wide range of environmental conditions, which is attributed to their metabolic versatility [STAL1991]. Cyanobacteria colonized successfully almost any illuminated environment on Earth, many of which are considered to be hostile for life. Cyanobacteria play a prominent role in many of these extreme environments.

Cyanobacteria to be discussed are:

  • Acaryochloris Marina
  • Nostoc Punctiforme
  • Prochlorococcus Marinus
  • Synechococcus Elongatus
  • Synechocystis Sp
  • Trichodesmium Erythraeum
Length

Figure 2.1: Genome Size of Cyanobacteria

Figure 2.1 shows a bar plot comparing the length (or size) of each cyanobacterial organism discussed in this section. The genome length constitutes the first statistical data in an organism.

[STANIER1962]Stanier, R.Y. and van Niel, C.B. (1962) The concept of a bacterium. Archiv fur Mikrobiologie 42, 17-35.
[KARL2002]Karl, D., Michaels, A., Bergman, B., Capone, D., Carpenter, E., Letelier, R., Lipschultz, F., Paerl, H., Sigman, D. and Stal, L. (2002) Dinitrogen fixation in the world’s oceans. Biogeochemistry 57/58, 47-98.
[STAL1991]Stal, L.J. (1991) The metabolic versatility of the mat-building cyanobacteria Microcoleus chthonoplastes and Oscillatoria limosa and its ecological significance. Algological Studies 64, 453-467.

Acaryochloris marina MBIC11017

Acaryochloris Marina

Figure 2.2: Acaryochloris marina

Photomicrograph of Acaryochloris marina. Credit: Phototrophic Prokaryotes Sequencing Project, via NCBI.

Is a marine cyanobacterium, was first isolated as an epiphyte of algae. Strains of A. marina been isolated from a variety of habitats and locations, usually associated with algae but also as free-living organisms. This cyanobacterium produces an atypical photosynthetic pigment, chlorophyll d, as the major reactive agent. The oxygenic photosynthesis based on this pigment may have evolved as an acclimatization to far-red light environments, or an as intermediate between the red-absorbing oxygenic and the far-red-absorbing anoxygenic photosynthesis that uses bacteriochlorophylls. Because of the unusual ratio of chlorophyll a to chlorophyll d in this organism, it has been used as a model to study the spectrographic characteristics of the two pigments. Acaryochloris marina MBIC11017 was isolated from algae from the coast of the Palau Islands in the western Pacific. This organism is been used for comparative analysis with other photosynthetic microorganisms.

Summary: Marine cyanobacterium, Kingdom: Bacteria, size: 6.5 Mb, Chromosome: 1, Plasmids: 9, Genome ID: 1179

Nostoc Punctiforme PCC 73102

Nostoc Punctiforme

Figure 2.3: Nostoc punctiforme

Nostoc. Credit: DOE Joint Genome Institute, via NCBI.

Is a Nitrogen-fixing plant symbiont, these genera of cyanobacteria are typically terrestrially-associated and are especially found in limestone or nutrient-poor soils. They are very similar to Anabaena spp. and historically they have been distinguished on the basis of morphological and life cycle characteristics. Nostoc spp. can grow heterotrophically or photoheterotrophically, and form heterocysts for nitrogen fixation.

This organism can form nitrogen-fixing symbiotic relationships with plants and fungi such as the bryophyte Anthoceros punctatus. The relationship is relatively simple as compared to the Rhizobial symbiotic relationship. In the presence of the plant, hormogonia (short motile filaments) infect the plant, and then form long heterocyst-containing (nitrogen-fixing differentiated bacterial cells) filaments. The bacterial cell receives carbon sources in exchange for fixed nitrogen.

Summary: Nitrogen-fixing plant symbiont, Kingdom: Bacteria, size: 8.23 Mb, Chromosome: 1, Plasmids: 5, Genome ID: 1050

Prochlorococcus Marinus MIT 9313

Prochlorococcus Marinus

Figure 2.4: Prochlorococcus Marinus

Prochlorococcus Marinus. Credit: C. Ting, J. King, C.W. Chisholm. DOE Joint Genome Institute, via NCBI.

This non-motile bacterium is a free-living marine organism that is one of the most abundant, as well as the smallest, on earth, and contributes heavily to carbon cycling in the marine environment. This cyanobacterium grows in areas of nitrogen and phosphorus limitation and is unique in that it utilizes divinyl chlorophyll a/b proteins as light-harvesting systems instead of phycobiliproteins. These pigments allow harvesting of light energy from blue wavelengths at low light intensity. There are two ecotypes, one that is low light adapted and one that is high light adapted.

Summary: Marine cyanobacterium, Kingdom: Bacteria, size: 2.41 Mb, Chromosome: 1, Genome ID: 164

Synechococcus Elongatus PCC 7942

Synechococcus

Figure 2.5: Synechococcus Elongatus

Synechococcus Elongatus. Credit: L.A. Sherman, D.M. Sherman. Purdue University, via NCBI.

These unicellular cyanobacteria are also known as blue green algae and along with Prochlorococcus are responsible for a large part of the carbon fixation that occurs in marine environments. Synechococcus have a broader distribution in the ocean and are less abundant in oligotrophic (low nutrient) regions. These organisms utilize photosystem I and II to capture light energy. They are highly adapted to marine environments and some strains have evolved unique motility systems in order to propel themselves towards areas that contain nitrogenous compounds. Motility may be due to the presence of spicules (long filaments) that extend from the cell surface and may act like oars during movement.

Synechococcus elongatus is an obligate photoautotroph, it has been studied extensively by an international research community with respect to acquisition of organic carbon, transport and regulation of nitrogen compounds, adaptation to nutrient stresses, and response to light intensity.

Summary: Marine cyanobacterium, Kingdom: Bacteria, size: 2.7 Mb, Chromosome: 1, Plasmids: 1, Genome ID: 430

Synechocystis Sp PCC 6803

Synechocystis

Figure 2.6: Synechocystis Sp.

Marie-Louise Lemloh, Jane Fromont, Franz Brummer and Kayley M Usher, “Synechocystis sp. Symbionts. Light microscopy image of two Synechocystis species in Mycale sp. 1: smaller green coccoid and larger red coccoid symbionts (indicated by arrow), scale bar = 10 micrometer” February 5, 2009 via Lemloh et al. BMC Ecology 2009 9:4 doi:10.1186/1472-6785-9-4, Creative Commons Attribution.

Synechocystis spp. are cyanobacterium that can grow both using photosynthesis as well as heterotrophically in the absence of light. These organisms serve as models for the uptake of carbon.

Synechocystis sp. PCC 6803 is the most popular cyanobacterial strain, serving as a standard in the research fields of photosynthesis, stress response, metabolism and so on. A glucose-tolerant (GT) derivative of this strain was used for genome sequencing at Kazusa DNA Research Institute in 1996, which established a hallmark in the study of cyanobacteria [TAJIMA2011].

Summary: Photosynthetic microorganism, Kingdom: Bacteria, size: 3.57 Mb, Chromosome: 1, Plasmids: 4, Genome ID: 1018

[TAJIMA2011]Tajima N, Sato S, Maruyama F, Kaneko T, Sasaki NV, Kurokawa K, Ohta H, Kanesaki Y, Yoshikawa H, Tabata S, Ikeuchi M, Sato N. Genomic structure of the cyanobacterium Synechocystis sp. PCC 6803 strain GT-S. DNA Res. 2011;18(5):393-9. Epub 2011 Jul 29. PubMed PMID: 21803841; PubMed Central PMCID: PMC3190959.

Trichodesmium Erythraeum IMS101

Trichodesmium Erythraeum

Figure 2.7: Trichodesmium Erythraeum

Trichodesmium Erythraeum. Credit: DOE Joint Genome Institute, via NCBI.

This filamentous marine cyanobacterium is a nitrogen-fixing organism that contributes a significant amount of the global fixed nitrogen each year. These bacteria are unusual in that nitrogen fixation takes place in a differentiated cell called the diazocyte which is different from the nitrogen-fixing differentiated cell (heterocyst) found in other cyanobacteria. The diazocyte is developed in order to protect the oxygen-sensitive nitrogenases and includes a number of changes including production of more membranes and down-regulation of photosynthetic activity during times of peak nitrogen fixation (noontime). This organism gives the Red Sea its name when large blooms appear and is one of the organisms most often associated with large blooms in marine waters.

Summary: Filamentous marine cyanobacterium, Kingdom: Bacteria, size: 7.75 Mb, Chromosome: 1, Genome ID: 1080

Algae

The term algae designates a most diverse and ancient group of organisms that is polyphyletic by evolution and artificial by taxonomy. Its only common feature is the ability to perform aerobic photosynthesis. Algae range by size from tiny cyanobacterial cells of the picoplankton to the giant kelps dominating rocky coastlines. They settle most diverse aquatic habitats such as hot springs and Arctic ice, live on and in rocks and various organisms, travel by air currents for thousands of miles and can be found in groundwater.

Algae to be discussed are:

  • Chlamydomonas Reinhardtii
  • Coccomyxa Subellipsoidea
  • Cyanidioschyzon Merolae
  • Ostreococcus Tauri (O. tauri)
  • Volvox Carteri
Length

Figure 2.8: Genome Size of Algae

Figure 2.8 shows a bar plot comparing the length (or size) of each algal organism discussed in this section.

Chlamydomonas Reinhardtii

Chlamydomonas Reinhardtii

Figure 2.9: Chlamydomonas Reinhardtii

Chlamydomonas Reinhardtii. Credit: Dr. Durnford, University of New Brunswick, via NCBI.

Chlamydomonas is a genus of unicellular green algae found widely in fresh water, on damp soil, and a few occur in the sea. The cells are spherical or ellipsoidal. They have two equal flagella, present at the anterior end of the cell. The cell is surrounded by a fibrous glycoprotein cell wall.

Chlamydomonas reinhardtii is the most commonly used laboratory species of Chlamydomonas since it can grow quickly with a generation time of 5 hrs and can form colonies on plates. In wild they survive in many different environments throughout the world. It is motile and cells of this species are haploid and can become diploid when deprived of nitrogen. Though photosynthetic, they can survive in total darkness in the presence of acetate. It has therefore been used as a model system to study photosynthesis and chloroplast biogenesis, mitochondrial biogenesis, flagellar assembly and motility, phototaxis, circadian rhythms, gametogenesis and mating, and cellular metabolism. Chlamydomonas reinhardtii has a genome size of about 120 Mb. It is haploid and has 17 chromosomes. It is an excellent system to study mutations as it has only a single copy of each gene.

Summary: Unicellular green alga, Kingdom: Eukaryotes, Size: 105.19 Mb, Haploid chromosomes: 17, Organelles: 2, Genome ID: 147

Coccomyxa Subellipsoidea C-169

Coccomyxa

Figure 2.10: Coccomyxa Subellipsoidea

Coccomyxa sp. NIES-2166 (aka C-169), Credit: The Microbial Culture Collection at NIES, Tsukuba, Japan, via NCBI.

Coccomyxa is a genus of unicellular green alga. It comprises of number of species that are free living but also has species that form symbiotic relationships with lichens. Coccomyxa sp. C-169 has an enzyme-digestible cell wall, which makes it an attractive research subject over some other strains. The Coccomyxa mitochondrial and plastid genome sequences are both circular-mapping and rich in G and C.

Summary: Unicellular green alga, Kingdom: Eukaryotes, Size: 48.83 Mb, Chromosomes: no data, Organelles: 1, Genome ID: 2692

Cyanidioschyzon Merolae

Cyanidioschyzon

Figure 2.11: Cyanidioschyzon Merolae

Cyanidioschyzon Merolae. Credit: Dr. T. Kuroiwa, University of Tokyo, via NCBI

Is a primitive, unicellular red alga with a compact genome and a simple gene composition. It lives in sulphate-rich, acidic hot waters. The cell contains a single nucleus, a single mitochondrion and a single chloroplast. The genome size is about 16 Mbp, smallest of all photosynthetic eukaryotes. The majority of genes do not include introns and smaller copy numbers are found for typically high-copy number genes such as ribosomal genes. Because of the simple gene composition, Cyanidioschyzon merolae genome provides a model system for studying the origin, evolution and fundamental mechanisms of eukaryotic cells.

Summary: Ultrasmall unicellular red alga, Kingdom: Eukaryotes, Size: 16.5 Mb, Haploid chromosomes: 20, Organelles: 2, Genome ID: 79

Ostreococcus tauri (O. tauri)

O. tauri

Figure 2.12: Ostreococcus tauri

Ostreococcus tauri. Credit: O.O. Banyuls-CNRS Courties, via NCBI

Is a small marine, photosynthetic organism measuring less than 1 mkm in size. It belongs to family Prasinophyceae which is believed to be the most primitive in the green lineage from which all other green algae, and ancestors of land plants have descended. It includes several photosynthetic picoeukaryotic organisms. O. tauri exhibits simple cellular structure with relatively large nucleus having one nuclear pore and a reduced cytoplasm with one chloroplast, one mitochondrion, and one Golgi body. It lacks flagella. O. tauri has a small genome of about 11.5 Mb with 14 or 18 chromosomes, which makes it an ideal organism for genome sequencing.

Summary: Free living, unicellular algae, Kingdom: Eukaryotes, Size: 12.45 Mb, Haploid chromosomes: 20, Organelles: 2, Genome ID: 373

Volvox Carteri 199

Volvox

Figure 2.13: Volvox Carteri

Volvox Carteri. Credit: David Kirk, Washington University, St. Louis, via NCBI

Volvox is a simple, spherical, multicellular green algae of order Volvocales. Volvocales are composed of two completely differentiated cell types, small somatic cells and few large, non motile reproductive cells. Volvox carteri is the commonly used lab species of Volvox. It has been extensively used for genetic analysis and evolutionary studies. Though it is haploid and asexual, it exhibits a sexual cycle that produces diploid zygotes which can withstand adverse conditions. It has an estimated genome size of about 120 Mb and Department of Energy’s Joint Genome institute is in the process of sequencing it. Sequence analysis of Volvox offers unique opportunity to study the genetic basis for evolution of multicellular organisms. Volvox was first discovered by van Leeuwenhoek in 1700.

Summary: Spherical, multicellular green alga, Kingdom: Eukaryotes, Size: 125.47 Mb, Haploid chromosomes: 14, Genome ID: 413

Higher Plants or Tracheophytes

Are vascular plants, their habitat is predominantly terrestrial or epiphytic. Their plastid pigments are Chlorophylls a, b; carotenoids (principally beta-carotene); xanthophylls (usually principally lutein). The cell wall components of tracheophytes are cellulose, hemicelluloses and lignin.

Their reproduction is through heteromorphic life cycle and sporophyte is the conspicuous phase, its growth is usually indeterminate. Sex organs are with or without a jacket of sterile cells, male gametes bi- or multiflagellate, or lacking flagella. Embryogeny is rarely exoscopic, embryo in many enclosed in a seed. Spores are rarely green, usually with well-defined wall (exine) impregnated with sporopollenin, often of two sizes, produced in different sporangia, the larger (megaspores) female and the smaller (microspores) male (heterospory). The specialized vegetative reproduction of the sporophyte is infrequent. Their growth forms are predominantly axial.

Higher plants to be discussed are:

  • Arabidopsis thaliana
  • Brachypodium Distachyon
  • Capsella rubella.
Legth

Figure 2.14: Genome Size of Algae

Figure 2.14 shows a bar plot comparing the length (or size) of each higher plant discussed in this section.

Arabidopsis thaliana (A. thaliana)

A. thaliana

Figure 2.15: Arabidopsis thaliana

Arabidopsis thaliana. Credit: Luca Comai, University of Washington, Seattle, via NCBI.

Is a small flowering plant of mustard family, brassicaceae (Cruciferae). It is distributed throughout the world and was first reported in the sixteenth century by Johannes Thal. It has been used for over fifty years to study plant mutations and for classical genetic analysis. It is now being used as a model organism to study different aspects of plant biology. A. thaliana is a diploid plant with 2n = 10 chromosomes. It became the first plant genome to be fully sequenced based on the fact that it has a small genome of ~120 Mb with a simple structure having few repeated sequences, short generation time of six weeks from seed germination to seed set, and produces large number of seeds.

It is an invaluable resource to agriculturally important crops, particularly to members of the same family, which includes canola, an important source of vegetable oil.

Summary: Small flowering plant of mustard family, Kingdom: Eukaryotes, Size: 119.15 Mb, Haploid chromosomes: 5, Organelles: 2, Genome ID: 4

Brachypodium Distachyon

Brachypoduim

Figure 2.16: Brachypodium Distachyon

Neil Harris (University of Alberta), “Brachypodium distachyon (L.) P.Beauv.” March 6, 2010 via Wikipedia, Creative Commons Attribution.

Brachypodium Distachyon is considered to be a model organism for the study of functional genomics in temperate grasses, cereals and dedicated biofuel crops. This status is a consequence of the attributes of small genome size (~355 Mbp), a small physical stature, self-fertility, a short life-cycle and accessions that are either diploid, tetraploid or hexaploid.

Summary: Model cereal, biofuel, Kingdom: Eukaryotes, Size: 271.92 Mb, Haploid chromosomes: 5, Organelles: 1, Genome ID: 698

Capsella rubella (C. rubella)

C. rubella

Figure 2.17: Capsella rubella

Capsella rubella Reut. Credit: Leo Michels, via irapl.altervista.org

Capsella rubella belongs to family Brassicaceae and is phylogenetically related to the model plant species Arabidopsis thaliana. Comparative mapping experiments by [ACARKAN2000] indicate extensive genome collinearity at the genetic and molecular level between the genomes of C. rubella and A. thaliana. C. rubella is a diploid species with n = 8 chromosomes. DOE Joint Genome Institute is planning to sequence the genome of C. rubella. Comparative analysis of the genomes of the two closely related species will be useful in understanding intra-species polymorphisms for A. thaliana.

Summary: A closely related genus of Arabidopsis, Kingdom: Eukaryotes, Size: 134.83 Mb, Haploid chromosomes: 8, Genome ID: 498

[ACARKAN2000]Acarkan A, Rossberg M, Koch M, Schmidt R. Comparative genome analysis reveals extensive conservation of genome organisation for Arabidopsis thaliana and Capsella rubella. Plant J. 2000 Jul;23(1):55-62. PubMed PMID: 10929101.

Footnotes

[SECKBACH2007]Seckbach J. (2007). “Algae and Cyanobacteria in Extreme Environments”. Springer.
[BARSANTI2005]Barsanti L. and Gualtieri P. (2005). “Algae: Anatomy, Biochemistry, and Biotechnology”. CRC Press.
[GRAHAM2000]Graham L.E. and Wilcox L.W. (2000). “Algae”. Prentice Hall.
[BELL2000]Bell P.R. and Hemsley A.R. (2000). “Green plants: their origin and diversity”. Cambridge University Press.
[HERRERO2008]Herrero A. and Flores E. (2008). “The cyanobacteria. Molecular biology, Genomics and Evolution”. Caister Academic Press.
[1]Organisms’ information has been taken from The National Center for Biotechnology Information (NCBI), Genome database.