



































Microsoft Word - 1028.doc


    

 Academic Journal of Science, Engineering and Technology 

Vol.6, Issue 2; March - April 2021; 

1252 Columbia Rd NW, Washington DC, United States 

https://topjournals.org/index.php/AJSET/index; mail: topacademicjournals@gmail.com 

  

 

 

1 | A c a d e m i c  J o u r n a l  o f  S c i e n c e ,  E n g i n e e r i n g  a n d  T e c h n o l o g y  

|  https://topjournals.org/index.php/AJSET 

EVOLUTIONARY INSIGHTS: COMPARATIVE ANALYSIS OF PORPHYRIN AND 

CHLOROPHYLL METABOLISM 

 

María Carmen García Rodríguez, Javier Antonio Pérez Martínez and Laura Isabel 

Fernández López 

 Department of Plant Biology I Plant Physiology, Faculty of Biology, Complutense University of Madrid Spain 

 

Abstract: Metabolic pathways represent intricate sequences of enzymatic reactions that underpin the remarkable 

phenomenon of cellular metabolism. This metabolic process, like all biological phenomena, has evolved over 

time, resulting in the diverse array of metabolic pathways found in living organisms. To unravel the evolutionary 

history of metabolism, comparative analyses of its constituent elements are essential. In this abstract, we explore 

the significance of comparative studies in reconstructing the evolutionary history of metabolism, highlighting the 

pioneering work of Cunchillos and Lecointre (2002, 2003, and 2005) in this domain. 

Keywords: Metabolic Pathways, Cellular Metabolism, Evolutionary History, Comparative Analysis, Enzymatic 

Reactions 

 

  

1. Introduction: A look back in time  

Metabolic pathways are a series of successive biochemical reactions catalyzed by enzymes which together 

constitute a process of extraordinary complexity, cellular metabolism. Like any other biological phenomenon, 

metabolism is the result of evolution.   

As the history of the species and their family relationships are derived from comparative studies, the history of 

metabolism can only be reconstructed through comparative analysis of its elements (Cunchillos and Lecointre, 

2002, 2003, 2005).  

Using the cladistic analysis to build an evolutionary hypothesis of the emergence and evolution of porphyrin and 

chlorophyll metabolism involves considering photosynthesis from the evolutionary point of view. On the origin 

of photosynthesis there are basically two hypotheses (Olson, 1999, 2001): one suggests that it originated in the 

prebiotic atmosphere of the Earth and comes to life; another, based on recent molecular phylogenetic analysis 

suggests that photosynthesis arose after chemolithotrophs organisms appear. However, we know little about how 

they were incorporated into the photosynthetic process its multiple biochemical components.  

The scientific community agrees that photosynthesis is a process that originates in bacteria because, firstly, there 

is no archaea with Mg-tetrapyrroles based photosystems and, secondly, photosynthetic eukaryota acquired this 

ability from cyanobacteria through endosymbiosis. It is possible to achieve a better understanding of the evolution 

of photosynthesis comparatively studying genes or gene products of photosynthesis in the groups of bacteria that 

synthesize photosystems: purple bacteria (proteobacteria, with photosystem II), green non-sulfur bacteria 

(photosystem II) , green sulfur bacteria (photosystem I), heliobacterias (photosystem I) and cyanobacteria 

(photosystems I and II). The Earth is about 4,500 million years and the beginning of life is in the Archean period, 

mailto:topacademicjournals@gmail.com


    

 Academic Journal of Science, Engineering and Technology 

Vol.6, Issue 2; March - April 2021; 

1252 Columbia Rd NW, Washington DC, United States 

https://topjournals.org/index.php/AJSET/index; mail: topacademicjournals@gmail.com 

  

 

 

2 | A c a d e m i c  J o u r n a l  o f  S c i e n c e ,  E n g i n e e r i n g  a n d  T e c h n o l o g y  

|  https://topjournals.org/index.php/AJSET 

about 3800-4000 million years ago. Stromatolites (the oldest Archaean fossils) containing evidence of biological 

carbon fixation have an approximate age of 3,800 million years (Schidiowski, 1988) while the oldest 

cyanobacteria-like cell microfossils have an age of 3,500 million years (Schopf, 1993; Schopf and Packer 1987), 

ie, appearing 300 million years after the first record of life.   

However, Earth was dominated at first by cyanobacteria which were 2,700 million years ago, coinciding with the 

first appearance of oxygen on earth (Des Marais, 2000). During approximately 1 million years, cyanobacteria 

increased the oxygen level to almost a quarter of the current level. The success of these organisms could be due 

not only to the power advantage of photosynthesis but due also to inhibition by oxygen (as toxicant) of potential 

competitors.   

The emergence of the first eukaryotes occurred about 1,800 million years ago, a fact that required 600-800 million 

years for cyanobacteria were incorporated by endosymbiosis in eukaryotes and evolved into chloroplasts. 

Thereafter the algae increased the oxygen level until present. Finally, his descendants land plants appeared 500 

million years ago.  

There is general consensus on the hypothesis suggesting the evolution of photosynthetic pigments from 

chemoautotrophs: they lived in an environment of chemical imbalance that led to the ability to use the pigments 

to harness light as an additional source of energy. Established photosynthesis, this might evolve to allow cells use 

sunlight as the only energy source (Nisbert and Sleep, 2001). On this tour it must be some intermediate stage that 

could be starring by purple bacteria: the anoxygenic photosynthesis bacteria evolve from this group who had 

phototaxis by infrared light (Nisbert et al., 1995).  

This hypothesis is based on the close relationship between the emission spectrum of geothermal light and 

absorption spectrum of bacteriochlorophylls b, relationship that serves the authors to raise the possibility that 

photosynthesis arose in organisms presenting bacteriochlorophylls a or b. They lived in the vicinity of oceanic 

hydrothermal vents where they could detect a faint infrared radiation.  

Accordingly, these phototaxis bacteria with the ability to detect infrared light have lived in an optimum 

environment which would have been an evolutionary advantage in terms of competition for resources or nutrients. 

Subsequently adaptation of this primitive photosystem would have allowed organisms to start using the far-red 

sunlight as it moved into shallower waters. Over time, chlorophylls appear to use light of higher energy (visible) 

and water photolysis. Photosynthesis in bacteria and plants occurs in two phases, photochemistry, and 

biochemistry. Photochemical phase involves the participation of photosynthetic pigments including chlorophylls 

and bacteriochlorophylls of bacteria and plants which are derived from the porphyrin metabolism.  

2. Map of metabolism of porphyrins and chlorophylls  

Porphyrins are tetrapyrroles binds covalently to a metal: iron (Fe) to form cytochromes, peroxidase, catalase, 

myoglobin and hemoglobin; copper (Cu) or nickel (Ni) to form molecules for electron transport in methanogenic 

bacteria; magnesium (Mg) to form chlorophylls and bacteriochlorophylls.  

In the porphyrin biosynthesis pathway (Fig. 1) there are two stages: 

1) Synthesis of 5-aminolevulinate (ALA): In all photosynthetic eukaryota and prokaryota, except the α-

proteobacteria, ALA is synthesized from glutamate which binds glutamyl-tRNA by glutamyl- tRNA synthase 

mailto:topacademicjournals@gmail.com


    

 Academic Journal of Science, Engineering and Technology 

Vol.6, Issue 2; March - April 2021; 

1252 Columbia Rd NW, Washington DC, United States 

https://topjournals.org/index.php/AJSET/index; mail: topacademicjournals@gmail.com 

  

 

 

3 | A c a d e m i c  J o u r n a l  o f  S c i e n c e ,  E n g i n e e r i n g  a n d  T e c h n o l o g y  

|  https://topjournals.org/index.php/AJSET 

catalyzed reaction (GluRS). Moreover, all non-photosynthetic eukaryota (animals, fungi and apicomplexa) and 

αproteobacteria form ALA by condensing glycine and succinyl-CoA in a reaction catalyzed by ALA synthase.  

2) Synthesis of protoporphyrin IX from 5-aminolevulinate (ALA), a chain of six reactions, the same in all 

organisms   

Figure 1: Porphyrins and chlrophylls biosynthesis pathway (Modified from GenomeNet) (red arrows 

indicate enzymes that undergo a single change in the analysis)  

  

mailto:topacademicjournals@gmail.com


    

 Academic Journal of Science, Engineering and Technology 

Vol.6, Issue 2; March - April 2021; 

1252 Columbia Rd NW, Washington DC, United States 

https://topjournals.org/index.php/AJSET/index; mail: topacademicjournals@gmail.com 

  

 

 

4 | A c a d e m i c  J o u r n a l  o f  S c i e n c e ,  E n g i n e e r i n g  a n d  T e c h n o l o g y  

|  https://topjournals.org/index.php/AJSET 

In the context of evolution it is important to highlight the conceptual difference between "evolution of 

photosynthesis" and "evolution of photosynthetic organisms": the evolution of photosynthesis involves a limited 

number of genes and / or gene products while the evolution of photosynthetic organisms involves the complete 

genome. The phylogeny of the 16S subunit rRNA (Woese, 1987) establishes three domains: Archaea 

(archaebacteria), Bacteria (eubacteria) and Eucarya (eukaryotes). Although this classification was discussed by 

other authors (CavalierSmith, 1992), the fact is that other phylogenetic studies using new genomic and sequence 

data provide consistent results with all three domains. However, when phylogeny based on vertical inheritance 

genes (16S rRNA) and photosynthesis gene phylogenies are compared, inconsistencies appear showing that the 

former do not necessarily reflect the second: evolution of organisms versus evolution of genes.  

3. Cladistic analysis to approach the evolution of porphyrins metabolism  

For the comparative study of various types of entities (molecules, metabolism, organs, organisms, populations, 

behaviors, geographic distribution, ecosystems) different techniques are used all aimed at analyzing the similarity 

between the strains under study. Between different procedures, cladistic analysis provides a high degree of 

objectivity to study but all techniques provide useful and necessary information in the evolutionary context.     

The porphyrins and chlorophyll metabolism is a complex process involving numerous chemical reactions 

catalyzed by enzymes. Its structure (components and functions) in the diversity of organisms is a product of 

evolution and can only be reconstructed by comparing the components. Tetrapyrroles serve as electron carriers in 

all domains of life. Heme carrying proteins were postulated to have been present in the last common ancestor of 

Bacteria and Archaea.     

The application of the comparative method requires first determine the set of elements to compare. These elements 

are referred to as cladistic terminology "operational taxonomic units". They can refer to molecules or species, 

taxa in general.    In this particular case, the set of taxa to be compared is the metabolism of porphyrins and 

chlorophylls in a set of organisms that constitute the study group (Table 1). Taxon, that is, each organism 

metabolism study group, is defined by characters that are enzymes (Table 2) involved in this part of cellular 

metabolism (Fg.1).   

Enzymes can be present or absent in a particular taxon (the bchl gene is absent in archaebacteria and present in 

bacteria) which means that the same character may have different "versions" which are called "character state".   

Table 1: Study Group, metabolism of porphyrins and chlorophylls in 63 species  

ACRONYM  NAME OF THE SPECIES  DOMAIN  GROUP  

afu  Archaeoglobus fulgidus  Archaea  euryarchaea  

ago        Ashbya gossypii  Eukarya  fungi  

ana  Nostoc  Bacteria   cyanobacteria  

ape  Aeropyrum pernix  Archaea  crenarchaea  

ath      Arabidopsis thaliana   Eukarya  plant  

atu   Agrobacterium fabrum  Bacteria  -proteobacteria  

bja   Bradyrhizobium diazoefficiens  Bacteria  -proteobacteria  

mailto:topacademicjournals@gmail.com


    

 Academic Journal of Science, Engineering and Technology 

Vol.6, Issue 2; March - April 2021; 

1252 Columbia Rd NW, Washington DC, United States 

https://topjournals.org/index.php/AJSET/index; mail: topacademicjournals@gmail.com 

  

 

 

5 | A c a d e m i c  J o u r n a l  o f  S c i e n c e ,  E n g i n e e r i n g  a n d  T e c h n o l o g y  

|  https://topjournals.org/index.php/AJSET 

bsu  Bacillus subtilis  Bacteria  firmicutes  

buc   Buchnera aphidicola  Bacteria  -proteobacteria    

cac  Clostridium acetobutylicum  Bacteria  firmicutes  

cal      Candida albicans  Eukarya  fungi  

cau  Chloroflexus aurantiacus  Bacteria  chloroflexi  

cch  Chlorobium chlorochromatii  Bacteria  chlorobi  

cel      Caenorhabditis elegans  Eukarya  metazoa  

cho     Cryptosporidium hominis  Eukarya  alveolata  

cme    Cyanidioschyzon merolae  Eukarya  rodofite  

cne     Cryptococcus neoformans  Eukarya  fungi  

cte  Chlorobium tepidum  Bacteria  chlorobi  

ddi     Dictyostelium discoideum  Eukarya  amebozoa  

det  Dehalococcoides mccartyi  Bacteria  chloroflexi  

dge  Deinococcus geothermalis  Bacteria   deinococus  

dme  Drosophila melanogaster  Eukarya  metazoa  

eco   Escherichia coli  Bacteria   -proteobacteria  

gox   Gluconobacter oxydans  Bacteria  -proteobacteria  

gvi  Gloeobacter violaceus  Bacteria  cyanobacteria  

hal  Halobacterium sp. NRC-1  Archaea  euryarchaea  

hbu  Hyperthermus butylicus  Archaea  crenarcheae  

hin   Haemophilus influenzae  Bacteria  -proteobacteria  

lic  Leptospira interrogans  Bacteria  spirochetae  

lpf   Legionella pneumophila  Bacteria  -proteobacteria  

mac  Methanosarcina acetivorans  Archaea  euryarchaea  

mca   Methylococcus capsulatus  Bacteria   -proteobacteria  

mga  Mycoplasma gallisepticum  Bacteria  mollicutes  

mja  Methanocaldococcus jannaschii  Archaea  euryarchaea  

mka  Methanopyrus kandleri  Archaea  euryarchaea  

mth  Methanothermobacter 

thermautotrophicus  

Archaea  euryarchaea  

mtu  Mycobacterium tuberculosis  Bacteria  actinobacteria  

neq  Nanoarchaeum equitans  Archaea  nonarchaea  

mailto:topacademicjournals@gmail.com


    

 Academic Journal of Science, Engineering and Technology 

Vol.6, Issue 2; March - April 2021; 

1252 Columbia Rd NW, Washington DC, United States 

https://topjournals.org/index.php/AJSET/index; mail: topacademicjournals@gmail.com 

  

 

 

6 | A c a d e m i c  J o u r n a l  o f  S c i e n c e ,  E n g i n e e r i n g  a n d  T e c h n o l o g y  

|  https://topjournals.org/index.php/AJSET 

neu   Nitrosomonas europaea  Bacteria  -proteobacteria  

nwi   Nitrobacter winogradskyi  Bacteria  -proteobacteria  

pab  Pyrococcus abyssi  Archaea  euryarchaea  

pac  Propionibacterium acnes  Bacteria  actinobacteria  

pae   Pseudomonas aeruginosa  Bacteria  -proteobacteria  

pai  Pyrobaculum aerophilum  Archaea  crenarchaea  

pfa  Plasmodium falciparum  Eukarya  alveolata  

plt  Prevotella intermedia  Bacteria  bacteroidete  

ppr   Photobacterium profundum  Bacteria  -proteobacteria  

rme   Cupriavidus metallidurans  Bacteria  -proteobacteria  

rpa   Rhodopseudomonas palustris  Bacteria  -proteobacteria  

rpr   Rickettsia prowazekii  Bacteria  -proteobacteria  

rru   Rhodospirillum rubrum  Bacteria  -proteobacteria  

sce  Saccharomyces cerevisiae  Eukarya  fungi  

sso  Sulfolobus solfataricus  Archaea  crenarchaea  

syc  Synechococcus elongatus  Bacteria  cyanobacteria  

syn  Synechocystis sp.  Bacteria  cyanobacteria  

tac  Thermoplasma acidophilum  Archaea  euryarchaea  

tbd   Thiobacillus denitrificans  Bacteria  -proteobacteria  

tcr  Trypanosoma cruzi  Eukarya  euglenozoa  

tde  Treponema denticola  Bacteria  spirochetae  

tel  Thermosynechococcus elongatus  Bacteria  cyanobacteria  

tth  Thermus thermophilus  Bacteria  deinococcus  

zmo   Zymomonas mobilis  Bacteria  -proteobacteria  

 

Table 2: Enzymes, characters selected in the study group  

Data code  ENZYME NAME  EC  GENE NAME  

B/ 1  5-aminolevulinate synthase  2.3.1.37  ALAS, HemA  

C/ 2  glutamyl-tRNA synthetase  6.1.1.17  gltX, others  

D/ 3  glutamyl-tRNA reductase  1.2.1.70  HemA  

E/ 4  glutamate-1-semialdehyde 2,1-

aminomutase  

5.4.3.8  HemL  

mailto:topacademicjournals@gmail.com


    

 Academic Journal of Science, Engineering and Technology 

Vol.6, Issue 2; March - April 2021; 

1252 Columbia Rd NW, Washington DC, United States 

https://topjournals.org/index.php/AJSET/index; mail: topacademicjournals@gmail.com 

  

 

 

7 | A c a d e m i c  J o u r n a l  o f  S c i e n c e ,  E n g i n e e r i n g  a n d  T e c h n o l o g y  

|  https://topjournals.org/index.php/AJSET 

F/ 5  porphobilinogen synthase  4.2.1.24  HemB  

G/ 6  hydroxymethylbilane synthase   2.5.1.61    HemC  

H/ 7  uroporphyrinogen-III synthase  4.2.1.75  HemD  

I/ 8  uroporphyrinogen decarboxylase  4.1.1.37   HemE  

J/ 9  uroporphyrinogen methyltransferase  2.1.1.107  HemX, CysG, 

CobA  

K/ 10  precorrin-2 dehydrogenase  1.3.1.76   CysG  

L/ 11  sirohydrochlorin ferrochelatase  4.99.1.4   CysG  

M/ 12  sirohydrochlorin cobaltochelatase  4.99.1.3  CbiX, CbiK  

N/ 13  cobalt-factor II C20-methyltransferase  2.1.1.151  CbiL, CbiL, CbiF  

O/ 14  precorrin-3 methyltransferase  2.1.1.131  CbiH, CbiL,CobJ  

P/ 15   precorrin-3 methylase  2.1.1.133  CbiF, CobM  

Q/ 16  precorrin-6A reductase  1.3.1.54  CobL, CobK  

S/ 17  precorrin-6 methyltransferase  2.1.1.132   CbiE, CbiT, CobL  

T/ 18  precorrin isomerase  5.4.1.2   CobH, CbiC  

U/ 19  cob(II)yrinic acid a,c-diamide 

reductase  

1.16.8.1    

V/ 20  cob(I)yrinic acid a,c-diamide  2.5.1.17  CobO, CobA, 

BtuR  

 adenosyltransferase    

W/ 21  adenosylcobyric acid synthase 

(glutaminehydrolysing  

6.3.5.10   CbiP, CobQ  

X/ 22  adenosylcobinamide-phosphate 

synthase  

6.3.1.10  CobD, CbiB  

Y/ 23  Adenosylcobinamide kinase  2.7.1.156   CobU, CobP  

Z/ 24  adenosylcobinamide-GDP 

ribazoletransferase  

2.7.8.26   CobS  

AA/  25  alpha-ribazole phosphatase  3.1.3.73   CobC  

AB/  26  cob(I)yrinic acid a,c-diamide 

adenosyltransferase  

2.5.1.17     

AC/  27  aquacobalamin reductase  1.16.1.3     

AD/  28  precorrin-2 C20-methyltransferase  2.1.1.130  CbiL, CobI  

mailto:topacademicjournals@gmail.com


    

 Academic Journal of Science, Engineering and Technology 

Vol.6, Issue 2; March - April 2021; 

1252 Columbia Rd NW, Washington DC, United States 

https://topjournals.org/index.php/AJSET/index; mail: topacademicjournals@gmail.com 

  

 

 

8 | A c a d e m i c  J o u r n a l  o f  S c i e n c e ,  E n g i n e e r i n g  a n d  T e c h n o l o g y  

|  https://topjournals.org/index.php/AJSET 

AE/  29  precorrin-3B synthase  1.14.13.83  CobG  

AF/  30  precorrin-6A synthase (deacetylating)  2.1.1.152    CobF  

AG/  31  coproporphyrinogen oxidase  1.3.3.3   HemF  

AH/  32  coproporphyrinogen dehydrogenase  1.3.99.22   HemN  

AJ/  33  protoporphyrinogen oxidase  1.3.3.4  HemG  

AK/  34  protoporphyrin IX magnesium-

chelatase  

6.6.1.1   Chld, Bchl  

AL/  35  magnesium protoporphyrin IX 

methyltransferase  

2.1.1.11  Chl, Bchl  

AM/  36  Mg-protoporphyrin IX monomethyl 

ester (oxidative) cyclase  

1.14.13.81  Acs, Pni  

AN/  37  protochlorophyllide reductase  1.3.1.33    

AO / 38  chlorophyllase  3.1.1.14     

AP / 39  chlorophyll synthase  2.5.1.62     

AQ / 40  ferrochelatase  4.99.1.1   HemH  

AR/  41  ferroxidase; ceruloplasmin  1.16.3.1    

AS /  42  cytochrome c heme-lyase  4.4.1.17     

AT / 43  heme oxygenase  1.14.99.3      

AU / 44  phytochromobilin:ferredoxin 

oxidoreductase  

1.3.7.4     

AV / 45  phycocyanobilin:ferredoxin 

oxidoreductase  

1.3.7.5     

AW / 46  15,16-dihydrobiliverdin:ferredoxin 

oxidoreductase  

1.3.7.2     

AX / 47  phycoerythrobilin:ferredoxin 

oxidoreductase  

1.3.7.3     

AY / 48  biliverdin reductase  1.3.1.24     

AZ / 49  bilirubin oxidase  1.3.3.5     

BA / 50  bilirubin UDP-glucuronosyltransferase  2.4.1.17     

BB / 51  beta-glucuronidase  3.2.1.31    

 

 The absence or presences of an enzyme in the metabolism of organisms that constitute the study group are discrete 

characters that are encoded in a binary system,  

mailto:topacademicjournals@gmail.com


    

 Academic Journal of Science, Engineering and Technology 

Vol.6, Issue 2; March - April 2021; 

1252 Columbia Rd NW, Washington DC, United States 

https://topjournals.org/index.php/AJSET/index; mail: topacademicjournals@gmail.com 

  

 

 

9 | A c a d e m i c  J o u r n a l  o f  S c i e n c e ,  E n g i n e e r i n g  a n d  T e c h n o l o g y  

|  https://topjournals.org/index.php/AJSET 

0 or 1. This coding means that an enzyme can be in two states: 0-absent or 1-present.  

Data have been collected from KEGG: Kyoto Encyclopedia of Genes and Genomes (1995-2015 Kanehisa 

Laboratories)  

The set of taxa and characters are reflected in a "matrix data" showing taxa in rows and states of a character in 

columns (Tale 3). This matrix is the basis for further analysis.  

Table 3: Data Matrix showing the states of the characters (0-absent enzyme, 1- present enzyme)   

  

  
Table 3. cont.  

mailto:topacademicjournals@gmail.com


Pérez-Urria, Elena & Avalos, Adolfo                                                                                    10  

  

  

10 | A c a d e m i c  J o u r n a l  o f  S c i e n c e ,  E n g i n e e r i n g  a n d  T e c h n o l o g y  

|  https://topjournals.org/index.php/AJSET 

 
A data matrix as the above in which the reflected characters are metabolic enzymes in two states, present (1) or 

absent (0), serves for the cladistic analysis of enzymes and accordingly the metabolism of porphyrins and 

chlorophylls in organisms of the study group.   

The cladistic analysis was performed with the MIX program in Phylip (Felsestein, 2001) 

(http://evolution.genetics.washington.edu/phylip.html) which estimates phylogenies by Wagner parsimony 

method for discrete character data with two states (0 and 1) (also available an online version of the program 



Pérez-Urria, Elena & Avalos, Adolfo                                                                                    11  

  

  

11 | A c a d e m i c  J o u r n a l  o f  S c i e n c e ,  E n g i n e e r i n g  a n d  T e c h n o l o g y  

|  https://topjournals.org/index.php/AJSET 

http://mobyle.pasteur.fr/cgi-bin/portal.py#jobs::overview).  Cladograms and trees are drawn with PHY.FI 

application (Fredslund, 2006).     

The result of this analysis is reflected by a cladogram representing an evolutionary hypothesis discussed below.   

4. One hypothesis about the evolution of porphyrins and chlorophylls  

The cladistic analysis following Wagner Parsimony Method for discrete characters in two states provides 100 

equally parsimonious trees (L = 233). Figure 2 shows the majority rule consensus tree and Figure 3 shows the 

strict consensus tree of the 100 most parsimonious and equally parsimonious trees.   

In the majority rule consensus tree two large groups or clades are observed: one formed by Bacteria and Archaea 

and another group of Bacteria and Eukaryota (Fig. 2). This result is confirmed by the strict consensus tree (Fig. 

3). The ancestral metabolism corresponds to Nanoarchaeum equitans (neq) leaving immediately after the ancestor 

(anc, the hypothetical ancestor with all characters set to 0, plesiomorphic, ie, absent).  

All enzymes considered undergo at least one change of state. Those experiencing a single change (bold in the 

Table 2) are apomorphic characters which define well metabolism (red arrows in Fig. 1). All other enzymes 

experience more than one change, they are homoplasy, indicate convergent evolution, the adaptive nature of 

metabolism and its components.  

In the clade Metabolism [BACTERIA + ARCHAEA] the group of cyanobacteria (tel, gvi, syn, ana and syc) is 

well defined by the enzyme phycocyanobilin:ferredoxin oxidoreductase (EC 1.3.7.5)  which experience a 

unique change and is a sinapomorphic character for the cyanobacteria clade. Within this group of cyanobacteria, 

Gloeobacter violaceus (gvi) is defined by two apomorphic characters: enzymes 15,16-

dihydrobiliverdin:ferredoxin oxidoreductase (EC 1.3.7.2) and phycoerythrobilin:ferredoxin 

oxidoreductase (EC 1.3.7.3).    

On the basis of this group of cyanobacteria, in a previous node, is the metabolism of Chloroflexus aurantiacus 

(cau) defined by an autoapomorphy, the bilirubin oxidase enzyme (EC 1.3.3.5). The clade Metabolism 

[BACTERIA + EUKARYA] includes among eukaryotes Arabidopsis thaliana (ath), plant whose metabolism is 

well defined by two apomorphies, enzymes chlorophyllase (EC 3.1.1.14) and phytochromobilin: ferredoxin 

oxidoreductase (EC 1.3.7.4).  

All other groups or clades are not based on apomorphic characters, no homologies to well define species 

metabolism. Therefore they are analogies and a case of convergent or parallel evolution. The similarity is due to 

homology and analogy. But nevertheless analogies or homoplasies not serve to discover phylogenetic 

relationships. Therefore they can not be established assumptions about relationships between sister groups based 

on the metabolism of porphyrins and chlorophylls.  

Resulting cladograms both majority consensus as strict consensus (Figs. 2 and 3)  reflects relationships derived 

from adaptive changes that lead to the expression, or not, of a gene and possible synthesis or catalytic activity of 

an enzyme as well as the acquisition or loss metabolic capabilities as an adaptive response to the environment. 

Moreover, lateral gene transfer is a key process in the early stages of cellular evolution that draws a complex 

network of relationships that mask and / or replace the vertical transfer and evolution model based on ancestry 

with modification.  On the other hand, much of the diversity found in algae is due to secondary and tertiary 

endosymbiotic events (Keeling, 2010).  



Pérez-Urria, Elena & Avalos, Adolfo                                                                                    12  

  

  

12 | A c a d e m i c  J o u r n a l  o f  S c i e n c e ,  E n g i n e e r i n g  a n d  T e c h n o l o g y  

|  https://topjournals.org/index.php/AJSET 

 



Pérez-Urria, Elena & Avalos, Adolfo                                                                                    13  

  

  

13 | A c a d e m i c  J o u r n a l  o f  S c i e n c e ,  E n g i n e e r i n g  a n d  T e c h n o l o g y  

|  https://topjournals.org/index.php/AJSET 

 The metabolism compared in the study group makes clear enzymes that change once. Some of these elements as 

apomorphic homologies could be phylogenetic markers. This is the case of phycocyanobilin:ferredoxin 

oxidoreductase (EC 1.3.7.5) for cyanobacteria and chlorophyllase (EC 3.1.1.14) for plants. 

Green algae and its progeny lost the cyanobacterial phycobilisome lightharvesting system, whereas red algae 

(cme, Cyanidioschyzon merolae) (on the cladogram with Arabidopsis thaliana)  and glaucophytes retained it. The 

chloroplasts in algae  and plants are derived from cyanobacteria and endosymbiosis gave rise to photosynthetic 

eukaryotes (Margulis, 1992). The evolution of photosynthesis is a complex process involving different sources 

and routes of its many components, so that its history can not be described as a simple, linear process. However, 

it seems certain that the emergence of Mg-tetrapyrrole and apoproteins of the reaction centers are key events that 

led to the development of the photosynthetic process. The flow of electrons acceptor—is channeled by protein 

complexes that always contain metallo-organic cofactors. Membrane-bound complexes couple the transfer of 

electrons across the membrane to the generation of an ion gradient and transmembrane electrical potential. This 

chemiosmotic mechanism was likely present in the last common ancestor and has been carried forward to the 

three presently persisting domains of life, Bacteria, Archaea, and Eukarya (Lane et al., 2010).   

The Granick (Granick, 1965) and Retrograde (Horowitz, 1945) hypotheses on the establishment of metabolic 

pathways are complementary. Granick established as hypotheses that the intermediate compounds of the modern 

biosynthetic pathways were the final products of early pathways and thus the evolution of the pathway can be 

traced from the beginning to the end. However this contrasts with the retrograde hypothesis which posits that 

present biosynthetic pathways are set up in the reverse order to their evolutionary history and occurred through 

gene duplications. But The Granick and retrograde hypotheses are not mutually exclusive because the retrograde 

hypothesis is a consequence of the depletion of base molecules present in the primordial soup, molecules that 

follow the Granick hypothesis may be more derived.  

There are still many aspects of the evolution of photosynthesis unresolved due in part to the existence of highly 

diversified components (Fig.4).  One way to learn more about this issue is to address the systematic, descriptive 

and comparative study of genes and gene products of photosynthesis in the diversity of phototrophic organisms. 

For this purpose contributes undoubtedly the availability of numerous molecular data and the use of phylogenetic 

analysis tools. For example and based on the results of this study, comparative analysis of enzymes glutamyl-

tRNA synthetase (EC 6.1.1.17), porphobilinogen synthase (EC 4.2.1.24) and protoporphyrinogen oxidase  (EC 

1.3.3.4) arises With all this new knowledge will continue to emerge thus reconstruct the evolutionary history of 

photosynthesis.  



Pérez-Urria, Elena & Avalos, Adolfo                                                                                    14  

  

  

14 | A c a d e m i c  J o u r n a l  o f  S c i e n c e ,  E n g i n e e r i n g  a n d  T e c h n o l o g y  

|  https://topjournals.org/index.php/AJSET 

Figure 4: Some molecules of metabolism of porphyrins and chlorophylls  

 
5. References  

Cavalier-Smith, T. (1992). Bacteria and Eucaryotes. Nature, 356: 570.  

Cunchillos, C. y Lecointre, G. (2002). Early steps of metabolism evolution inferred by cladistic analysis of amino 

acid catabolic pathways. C.R. Biologies, 325: 119129.  

Cunchillos, C. y Lecointre, G. (2003). Evolution of Amino Acid Metabolism inferred through Cladistic Analysis. 

The Journal of Biological Chemistry, 278 (48), nov.: 47960-47970.  

Cunchillos, C. y Lecointre, G. (2005). Integrating the Universal Metabolism into a Phylogenetic Analysis. Mol. 

Biol. Evol., 22 (1): 1-11.  

Des Marais, D.J. (2000). When did photosynthesis emerge on Earth? Science, 289: 1703-1705.  

Enzyme Nomenclature (1973). Recommendations (1972) of the International Union of Pure and Applied 

Chemistry and The International Union of Biochemistry. Elsevier Scientific Publishing Company, 

Amsterdam.  

Felsenstein, J. (2001). PHYLIP (phylogeny inference package). version 3.6a3. Department of Genetics. 

University of Washington, Seattle.  

Fredslund,  J. (2006).  PHY·FI: fast and easy online creation and manipulation of phylogeny color figures. BMC 

Bioinformatics 7:315.  



Pérez-Urria, Elena & Avalos, Adolfo                                                                                    15  

  

  

15 | A c a d e m i c  J o u r n a l  o f  S c i e n c e ,  E n g i n e e r i n g  a n d  T e c h n o l o g y  

|  https://topjournals.org/index.php/AJSET 

Granick,  S. 1965. Evolution of heme and chlorophyll. In Evolving Genes and Proteins, ed. V Bryson, HJ Vogel, 

pp. 67–88. New York: Academic.  

Horowitz, N.J. 1945. On the evolution of biochemical synthesis. Proc. Natl. Acad. Sci. USA 31:153–57  

KEGG: Kyoto Encyclopedia of Genes and Genomes 1995-2015 Kanehisa Laboratories. Available on 

http://www.genome.jp/kegg/    

Keeling, P.J. 2010. The endosymbiotic origin, diversification and fate of plastids. Philos. Trans. R. Soc. Lond. B 

365:729–48.  

Lane, N, Allen, J.F, Martin, W. 2010. How did LUCA make a living? Chemiosmosis in the origin of life. 

BioEssays 32:271–80.  

Margulis,  L. 1992. Symbiosis in Cell Evolution. San Francisco: Freeman.  

Nisbert, E.G. y Sleep, N.H. (2001). The habitat and nature of early life. Nature, 409: 1083-1091.  

Olson, J.M. (1999). Early evolution of chlorophyll-based photosystems. Chemtracts, 12: 468-482.  

Olson, J.M. (2001). Evolution of Photosynthesis (1970), re-examined thirty years later. Photosynth. Res., 68:95-

112.  

Schidiowski, M. (1988). A 3.800-million-year isotopic record of life from carbon in sedimentary rocks. Nature, 

333: 313-318.  

Shopf J.W. (1993). Microfossils of the early archean apex chert: new evidence ofthe antiquity of life. Science, 

260: 640-646.  

Schopf, J.W. y Packer, B.M. (1987). Early Archean (3.3-billion to 3.5-billion year old) microfossils from 

Warrawoona Group. Australia. Science, 237: 70-73. Woese, C.R. (1987). Bacterial evolution. Microbiol. 

Rev., 51: 221-271. 


