Comparative analysis of proteomes in aerobic and anaerobic bacteria Aditya Kumar Pal, Tapash Chandra Ghosh Raiganj University, Department of Microbiology Raiganj 733134 Abstract
Results
Although oxygen is an essential elements for most of organisms but it can damage proteins. Several proteome adaptations had occurred to tackle these stresses and we assessed them using comparative genomics in a nonphylogenetic context. Among the four bases in DNA, guanine is the most susceptible to damage from oxidative stress. Replication of DNA containing damaged guanines makes G to T mutations and reduces the GC content. First, we find the oxidable amino acids (cysteine, methionine, tyrosine, phenylalanine, histidine, tryptophan) in aerobic, anaerobic, obligate aerobic, obligate anaerobic bacteria and found that most of them are present in very low amount in aerobes and obligate aerobes compared to anaerobes and obligate anaerobes. It is because of the aerobes are living in high oxidative stress while anaerobes are not in high oxidative stress. We also found the relation of oxidable amino acids with genomic GC content and found all have the relation with GC content except cysteine and methionine. These findings will be helpful in the further studies of evolutionary characteristics of aerobic and anaerobic bacteria.
2. Comparison of oxidable Amino acid frequencies in aerobes and anaerobes We observed an expected increasing trends from obligate aerobe to obligate anaerobe for cysteine , methionine , tyrosine and phenylalanine but observed a opposite trends for histidine and tryptophan.
Introduction Accumulation of oxygen was the most significant change in the evolution of all exposed organisms. Aerobic organisms uses oxygen (O2) for respiration. Reactive by products of oxygen, like- superoxide anion (O2–), hydrogen peroxide (H2O2), and hydroxyl radicals (OH-), are produced continuously in cells grown in presence of O2. There are some enzymes (superoxide dismutases (SOD), catalase) to tackle this oxygen stress in aerobes. Many genomic and proteome adaptations also occurred to tackle these stresses. We here compared the whole genome GC content among four types of bacterial species - aerobes, anaerobes, obligate aerobes and obligate anaerobes and also analyzed the frequency of five oxidable amino acids in aerobes, anaerobes, obligate aerobes and obligate anaerobes and also compared with their whole genome GC content to find any relation between GC % and oxidable amino acids contents. The avoidance of these oxidable amino acids, probably increases the genomic GC content in aerobes.
3. Nonphylogenetically controlled comparison showed higher GC content in obligate aerobes We found that most of the anaerobic species are present in 25 – 55 % GC content, while aerobes are found in the 60-80% GC range. Above 80% of obligate aerobes have the GC content of 60 – 80 %.
Methods 1. Retrieving Genomic and Proteomic Data In the Genomes Online Database (GOLD) , organisms are divided into four categories: aerobe, anaerobe, obligate aerobe, and obligate anaerobe. The GC contents of all the samples were obtained from the NCBI Genome database. The genome sequences of the species were retrieved from the NCBI genome database. We retrieved the proteome sequences of all these species from UniProt protein database.
3. Significance test Two tailed Mann Whitney U test calculator (Wilcoxon rank-sum) is used for the nonparametric test to find the higher significant results.
Results 1. Comparison of amino acid frequencies in aerobes and anaerobes nonphylogenetically We compared all 20 amino acid contents among 88 aerobic samples , 41 obligate aerobes , 87 anaerobic samples and 39 obligate anaerobes and found oxidable amino acids are present in very low amount than others ( glycine, lysine, alanine).
4. Relation of GC% with oxidable amino acids composition We observed that most of the amino acid frequencies are dependent with the GC content except Cysteine and Methionine. For cysteine and methionine there are no significant differences with the GC% variation ( P > 0.11 ), while other four oxidable amino acid shown a significant relation with GC% ( P < 0.0001 ) . (a) Relation of GC% with Oxidable amino acids in Aerobes 6 Tyrosine Phenylalanine Histidine Cysteine Tryptophan Methionine Amino Acid amount %
Amino acid frequencies are calculated by in house Perl programme.
4
2
0
GC %
<40
40-60
>60
(b) Relation of GC% with Oxidable amino acids in Anaerobes 6
Amino Acid amount %
2. Amino acid frequency calculation
Cysteine
Methionine
Tyrosine Phenylalanine
Histidine
Tryptophan
4 2 0
<40
40-60
>60
Conclusion We observed that aerobes and obligate aerobes have low content of cysteine, methionine, tyrosine and phenylalanine but have opposite trends for histidine and tryptophan. It might be due to having more GC rich codons for histidine and tryptophan but because of cysteine, methionine, tyrosine and phenylalanine are coded by mostly AT rich codons. Aerobes and obligate aerobes having higher GC content they have more histidine and tryptophan amino acids although those are oxidation susceptible.