**1. Introduction**

364 Biochemistry

Wang, S., Gong, Z., Chen, R., Liu, Y., Li, A., Li, G. & Zhou, J. (2009). JWA Regulates XRCC1

Watabe, M., Aoyama, K. & Nakaki, T. (2007). Regulation of Glutathione Synthesis Via

Watabe, M., Aoyama, K. & Nakaki, T. (2008). A Dominant Role of GTRAP3-18 in Neuronal

Waxman, E. A., Baconguis, I., Lynch, D. R. & Robinson, M. B. (2007). *N*-Methyl-*D*-Aspartate

Wilke, N., Sganga, M., Barhite, S. & Miles, M. F. (1994). Effects of Alcohol on Gene Expression in Neural Cells, *Experientia. Supplementum* Vol.71, pp. 49-59, ISSN 1023-294X Won, S. J., Yoo, B. H., Brennan, A. M., Shin, B. S., Kauppinen, T. M., Berman, A. E., Swanson,

Wu, Y., Chen, R., Zhao, X., Li, A., Li, G. & Zhou, J. (2011). JWA Regulates Chronic Morphine

Xia, P., Pei, G. & Schwarz, W. (2006). Regulation of the Glutamate Transporter EAAC1 by

Yang, W. & Kilberg, M. S. (2002). Biosynthesis, Intracellular Targeting, and Degradation of

Zerangue, N. & Kavanaugh, M. P. (1996). Interaction of L-Cysteine with a Human Excitatory

Zhou, J., Ye, J., Zhao, X. & Li, A. (2008). JWA Is Required for Arsenic Trioxide Induced

Zhu, T., Chen, R., Li, A. P., Liu, J., Liu, Q. Z., Chang, H. C. & Zhou, J. W. (2005). Regulation

K562 and MCF-7 Cells, *Journal of Biomedical Science* Vol.12, No.1, pp. 219-227 Zhu, Y., King, M. A., Schuller, A. G., Nitsche, J. F., Reidl, M., Elde, R. P., Unterwald, E.,

*Neuroscience* Vol.24, No.1, (July 2006), pp. 87-93, ISSN 0953-816X

*Pharmacology* Vol.72, No.5, (November 2007), pp. 1103-1110

1936-1950

pp. 9404-9413

17594-17607, ISSN 0021-9258

(Electronic), 0270-6474 (Linking)

0006-291X (Linking)

419-423, ISSN 0022-3751

6273 (Linking)

No.1, (July 2008), pp. 33-40, ISSN 0041-008X

and Functions as a Novel Base Excision Repair Protein in Oxidative-Stress-Induced DNA Single-Strand Breaks, *Nucleic Acids Research* Vol.37, No.6, (April 2009), pp.

Interaction between Glutamate Transport-Associated Protein 3-18 (GTRAP3-18) and Excitatory Amino Acid Carrier-1 (EAAC1) at Plasma Membrane, *Molecular* 

Glutathione Synthesis, *The Journal of Neuroscience* Vol.28, No.38, (September 2008),

Receptor-Dependent Regulation of the Glutamate Transporter Excitatory Amino Acid Carrier 1, *The Journal of Biological Chemistry* Vol.282, No.24, (June 2007), pp.

R. A. & Suh, S. W. (2010). EAAC1 Gene Deletion Alters Zinc Homeostasis and Exacerbates Neuronal Injury after Transient Cerebral Ischemia, *The Journal of Neuroscience* Vol.30, No.46, (November 2010), pp. 15409-15418, ISSN 1529-2401

Dependence Via the Delta Opioid Receptor, *Biochemical and Biophysical Research Communications* Vol.409, No.3, (June 2011), pp. 520-525, ISSN 1090-2104 (Electronic),

Expression and Activation of Delta-Opioid Receptor, *The European Journal of* 

the EAAC1 Glutamate/Aspartate Transporter in C6 Glioma Cells, *The Journal of Biological Chemistry* Vol.277, No.41, (October 2002), pp. 38350-38357, ISSN 0021-9258

Amino Acid Transporter, *The Journal of Physiology* Vol.493 (Pt 2), (June 1996), pp.

Apoptosis in HeLa and MCF-7 Cells Via Reactive Oxygen Species and Mitochondria Linked Signal Pathway, *Toxicology and Applied Pharmacology* Vol.230,

of a Novel Cell Differentiation-Associated Gene, JWA During Oxidative Damage in

Pasternak, G. W. & Pintar, J. E. (1999). Retention of Supraspinal Delta-Like Analgesia and Loss of Morphine Tolerance in Delta Opioid Receptor Knockout Mice, *Neuron* Vol.24, No.1, (Sep 1999), pp. 243-252, ISSN 0896-6273 (Print), 0896In addition to the most recently reported aerobic anoxygenic phototrophic bacterium *Chloroacidobacterium thermophilium* [1], five phyla of phototrophic bacteria have been reported, including four phyla anoxygenic phototrophic bacteria (anaerobic and aerobic anoxygenic phototrophic Proteobacteria, filamentous anoxygenic phototrophs (FAPs), green sulfur bacteria and heliobacteria) and oxygenic phototrophic bacteria (cyanobacteria). According to 16S rRNA analysis, *Chloroflexi* species in FAPs are the earliest branching bacteria capable of photosynthesis [2,3] (**Fig. 1**), and the thermophilic bacterium *Chloroflexus* [Cfl.] *aurantiacus* among the *Chloroflexi* species has been long regarded as a key organism to resolve the obscurity of the origin and early evolution of photosynthesis. *Cfl. aurantiacus* can grow phototrophically under anaerobic conditions or chemotrophically under aerobic and dark conditions [4]. During phototrophic growth of *Cfl. aurantiacus*, the light energy is first absorbed by the peripheral light-harvesting complex chlorosomes, then transferred to the integral membrane B808-866 core antenna complex and finally to the reaction center (RC). *Cfl. aurantiacus* contains a chimeric photosystem that comprises some characters of green sulfur bacteria (chlorosomes) and anoxygenic phototrophic Proteobacteria (the B808-866 core antenna complex), and also has some unique electron transport proteins compared to other photosynthetic bacteria. The complete genomic sequence of *Cfl. aurantiacus* has been recently determined, analyzed and compared to the genomes of other photosynthetic bacteria [5].

Significant contributions of horizontal/lateral gene transfer among uni-cellular [6] and multi-cellular [7] organisms during the evolution, including the evolution of photosynthesis [8,9], have been recognized. Various perspectives on evolution of photosynthesis have been reported in literature [8-25], whereas our understanding of transition from anaerobic to aerobic world is still fragmentary. The recent genomic report on *Cfl. aurantiacus* [5], along with previous physiological, ecological and biochemical studies, indicate that the anoxygenic phototroph bacterium *Cfl. aurantiacus* has many interesting and certain unique features in its metabolic pathways. The *Cfl. aurantiacus* genome contains numerous aerobic/anaerobic gene pairs and oxygenic/anoxygenic metabolic pathways in the *Cfl. aurantiacus* genome [5], suggesting numerous gene adaptations/replacements in *Cfl. aurantiacus* to facilitate life under both anaerobic and aerobic growth conditions. These

Fig. 1. Phylogenetic tree of photosynthetic bacteria.

The tree was constructed with un-rooted neighbor joining 16S rRNA dendrogram from five phyla of photosynthetic microbes, including cyanobacteria, heliobacteria, phototrophic anoxygenic Proteobacteria, green sulfur bacteria and filamentous anoxygenic phototrophs (FAPs). Bacterial names and accession numbers of 16S rRNA genes: (1) Phototrophic anoxygenic Proteobacteria: *Roseobacter denitrificans* OCh114 (CP000362), *Roseobacter litoralis* (X78312), *Rhodobacter capsulatus* (D16428), *Rhodobacter sphaeroides* 2.4.1 (X53853), *Rhodopseudomonas faecalis* strain gc (AF123085), *Rhodopseudomonas palustris* (D25312), *Rhodopseudomonas acidophila* (FR733696), *Rhodopseudomonas viridis* DSM 133 (AF084495), *Rubrivivax gelatinosus* (D16213); (2) heliobacteria: *Heliobacterium gestii* (AB100837), *Heliobacterium modesticaldum* (CP000930); (3) cyanobacteria: *Oscillatoria amphigranulata* str. 19- 2 (AF317504), *Oscillatoria amphigranulata* str. 11-3 (AF317503), *Oscillatoria amphigranulata* str. 23-3 (AF317505), *Microcystis aeruginosa* NIES-843 (AP009552), *Nostoc azollae* 0708 (NC\_014248); (4) green sulfur bacteria: *Chlorobaculum thiosulfatiphilum* DSM 249 (Y08102), *Pelodictyon luteolum* DSM 273 (CP000096), *Chlorobium limicola* DSM 245 (CP001097), *Chlorobaculum tepidum* TLS (M58468), *Chlorobium vibrioforme* DSM 260 (M62791); and (5) FAPs: *Chloroflexus aurantiacus* J-10-fl (M34116), *Chloroflexus aggregans* (D32255), *Oscillochloris trichoides* (AF093427), *Roseiflexus castenholzii* DSM 13941 (AB041226)

The tree was constructed with un-rooted neighbor joining 16S rRNA dendrogram from five phyla of photosynthetic microbes, including cyanobacteria, heliobacteria, phototrophic anoxygenic Proteobacteria, green sulfur bacteria and filamentous anoxygenic phototrophs (FAPs). Bacterial names and accession numbers of 16S rRNA genes: (1) Phototrophic anoxygenic Proteobacteria: *Roseobacter denitrificans* OCh114 (CP000362), *Roseobacter litoralis*

*Heliobacterium modesticaldum* (CP000930); (3) cyanobacteria: *Oscillatoria amphigranulata* str. 19- 2 (AF317504), *Oscillatoria amphigranulata* str. 11-3 (AF317503), *Oscillatoria amphigranulata* str.

(NC\_014248); (4) green sulfur bacteria: *Chlorobaculum thiosulfatiphilum* DSM 249 (Y08102), *Pelodictyon luteolum* DSM 273 (CP000096), *Chlorobium limicola* DSM 245 (CP001097), *Chlorobaculum tepidum* TLS (M58468), *Chlorobium vibrioforme* DSM 260 (M62791); and (5) FAPs: *Chloroflexus aurantiacus* J-10-fl (M34116), *Chloroflexus aggregans* (D32255), *Oscillochloris* 

(X78312), *Rhodobacter capsulatus* (D16428), *Rhodobacter sphaeroides* 2.4.1 (X53853), *Rhodopseudomonas faecalis* strain gc (AF123085), *Rhodopseudomonas palustris* (D25312), *Rhodopseudomonas acidophila* (FR733696), *Rhodopseudomonas viridis* DSM 133 (AF084495), *Rubrivivax gelatinosus* (D16213); (2) heliobacteria: *Heliobacterium gestii* (AB100837),

23-3 (AF317505), *Microcystis aeruginosa* NIES-843 (AP009552), *Nostoc azollae* 0708

*trichoides* (AF093427), *Roseiflexus castenholzii* DSM 13941 (AB041226)

Fig. 1. Phylogenetic tree of photosynthetic bacteria.

include duplicate genes and gene clusters for the alternative complex III (ACIII) [26,27], auracyanin (a type I blue copper protein) [28,29] and NADH:quinone oxidoreductase (complex I); and several aerobic/anaerobic enzyme pairs in central carbon metabolism (pyruvate metabolism and the tricarboxylic acid (TCA) cycle) and tetrapyrroles and nucleic acids biosynthesis [5]. Overall, genomic information is consistent with a high tolerance for oxygen that has been reported in the growth of *Cfl. aurantiacus*.

Phylogenetic analyses on the photosystems and comparisons to the genome and reports of other photosynthetic bacteria suggest lateral or horizontal gene transfers between *Cfl. aurantiacus* and other photosynthetic bacteria [3,30,31]. The *Cfl. aurantiacus* genome suggests possible evolutionary connections of photosynthesis. Here we probe some proposed lateral gene transfers using the phylogenetic analyses on important proteins/enzymes on chlorophyll biosynthesis, photosynthetic electron transport chain, and central carbon metabolism. Further, we also discuss the evolutionary perspectives on assembling photosynthetic machinery, autotrophic carbon assimilation and unique components on the electron transport chains of *Cfl. aurantiacus* and other phototrophic and non-phototrophic bacteria.
