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Conservation analysis of the CydX protein yields insights into small protein identification and evolution.

Allen RJ, Brenner EP, VanOrsdel CE, Hobson JJ, Hearn DJ, Hemm MR - BMC Genomics (2014)

Bottom Line: Further investigation of cydAB operons identified two additional conserved hypothetical small proteins: CydY encoded in CydAQlong operons that lack cydX, and CydZ encoded in more than 150 CydAQshort operons.These results elucidate the prevalence of CydX throughout the Proteobacteria, provide insight into the selection pressure and sequence requirements for CydX function, and suggest a potential functional interaction between the small protein and the CydA Q-loop, an enigmatic domain of the cytochrome bd oxidase complex.Finally, these results identify other conserved small proteins encoded in cytochrome bd oxidase operons, suggesting that small protein subunits may be a more common component of these enzymes than previously thought.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Towson University, Towson 21252MD, USA. mhemm@towson.edu.

ABSTRACT

Background: The reliable identification of proteins containing 50 or fewer amino acids is difficult due to the limited information content in short sequences. The 37 amino acid CydX protein in Escherichia coli is a member of the cytochrome bd oxidase complex, an enzyme found throughout Eubacteria. To investigate the extent of CydX conservation and prevalence and evaluate different methods of small protein homologue identification, we surveyed 1095 Eubacteria species for the presence of the small protein.

Results: Over 300 homologues were identified, including 80 unannotated genes. The ability of both closely-related and divergent homologues to complement the E. coli ΔcydX mutant supports our identification techniques, and suggests that CydX homologues retain similar function among divergent species. However, sequence analysis of these proteins shows a great degree of variability, with only a few highly-conserved residues. An analysis of the co-variation between CydX homologues and their corresponding cydA and cydB genes shows a close synteny of the small protein with the CydA long Q-loop. Phylogenetic analysis suggests that the cydABX operon has undergone horizontal gene transfer, although the cydX gene likely evolved in a progenitor of the Alpha, Beta, and Gammaproteobacteria. Further investigation of cydAB operons identified two additional conserved hypothetical small proteins: CydY encoded in CydAQlong operons that lack cydX, and CydZ encoded in more than 150 CydAQshort operons.

Conclusions: This study provides a systematic analysis of bioinformatics techniques required for the unique challenges present in small protein identification and phylogenetic analyses. These results elucidate the prevalence of CydX throughout the Proteobacteria, provide insight into the selection pressure and sequence requirements for CydX function, and suggest a potential functional interaction between the small protein and the CydA Q-loop, an enigmatic domain of the cytochrome bd oxidase complex. Finally, these results identify other conserved small proteins encoded in cytochrome bd oxidase operons, suggesting that small protein subunits may be a more common component of these enzymes than previously thought.

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cydABXorganization and function inEscherichia coli. (A) Operon organization of the cydABX cytochrome bd oxidase operon. (B) Function of the CydABX complex in the electron transport chain.
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Fig1: cydABXorganization and function inEscherichia coli. (A) Operon organization of the cydABX cytochrome bd oxidase operon. (B) Function of the CydABX complex in the electron transport chain.

Mentions: Cytochrome oxidases are a broad family of integral membrane complexes that catalyze the terminal electron transfer in eubacterial and archaeal respiration [8]. These complexes couple the oxidation of either quinol or cytochrome c substrates with the reduction of O2 to water (Figure 1B). Cytochrome bd’s high O2 affinity allows it to efficiently scavenge oxygen to prevent damage to oxygen-sensitive enzymes, as well as permit growth in microaerobic and anaerobic environments. The complexes are also essential for survival under a number of stress conditions, including iron deficiency, nitrosative and peroxide stresses, exposure to cyanide, pressure, and high temperatures [9, 10]. Cytochrome bd oxidases support the Dsb pathway in catalyzing protein disulfide bonds for proper protein folding by re-oxidizing quinones reduced by DsbB in the activity of the pathway [11]. Furthermore, bd oxidases enhance the persistence of bacteria engulfed by macrophages [12], and are required for virulence of many bacterial pathogens [13, 14]. As such, cytochrome bd is under investigation as an antibiotic target [9].Figure 1


Conservation analysis of the CydX protein yields insights into small protein identification and evolution.

Allen RJ, Brenner EP, VanOrsdel CE, Hobson JJ, Hearn DJ, Hemm MR - BMC Genomics (2014)

cydABXorganization and function inEscherichia coli. (A) Operon organization of the cydABX cytochrome bd oxidase operon. (B) Function of the CydABX complex in the electron transport chain.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4325964&req=5

Fig1: cydABXorganization and function inEscherichia coli. (A) Operon organization of the cydABX cytochrome bd oxidase operon. (B) Function of the CydABX complex in the electron transport chain.
Mentions: Cytochrome oxidases are a broad family of integral membrane complexes that catalyze the terminal electron transfer in eubacterial and archaeal respiration [8]. These complexes couple the oxidation of either quinol or cytochrome c substrates with the reduction of O2 to water (Figure 1B). Cytochrome bd’s high O2 affinity allows it to efficiently scavenge oxygen to prevent damage to oxygen-sensitive enzymes, as well as permit growth in microaerobic and anaerobic environments. The complexes are also essential for survival under a number of stress conditions, including iron deficiency, nitrosative and peroxide stresses, exposure to cyanide, pressure, and high temperatures [9, 10]. Cytochrome bd oxidases support the Dsb pathway in catalyzing protein disulfide bonds for proper protein folding by re-oxidizing quinones reduced by DsbB in the activity of the pathway [11]. Furthermore, bd oxidases enhance the persistence of bacteria engulfed by macrophages [12], and are required for virulence of many bacterial pathogens [13, 14]. As such, cytochrome bd is under investigation as an antibiotic target [9].Figure 1

Bottom Line: Further investigation of cydAB operons identified two additional conserved hypothetical small proteins: CydY encoded in CydAQlong operons that lack cydX, and CydZ encoded in more than 150 CydAQshort operons.These results elucidate the prevalence of CydX throughout the Proteobacteria, provide insight into the selection pressure and sequence requirements for CydX function, and suggest a potential functional interaction between the small protein and the CydA Q-loop, an enigmatic domain of the cytochrome bd oxidase complex.Finally, these results identify other conserved small proteins encoded in cytochrome bd oxidase operons, suggesting that small protein subunits may be a more common component of these enzymes than previously thought.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Towson University, Towson 21252MD, USA. mhemm@towson.edu.

ABSTRACT

Background: The reliable identification of proteins containing 50 or fewer amino acids is difficult due to the limited information content in short sequences. The 37 amino acid CydX protein in Escherichia coli is a member of the cytochrome bd oxidase complex, an enzyme found throughout Eubacteria. To investigate the extent of CydX conservation and prevalence and evaluate different methods of small protein homologue identification, we surveyed 1095 Eubacteria species for the presence of the small protein.

Results: Over 300 homologues were identified, including 80 unannotated genes. The ability of both closely-related and divergent homologues to complement the E. coli ΔcydX mutant supports our identification techniques, and suggests that CydX homologues retain similar function among divergent species. However, sequence analysis of these proteins shows a great degree of variability, with only a few highly-conserved residues. An analysis of the co-variation between CydX homologues and their corresponding cydA and cydB genes shows a close synteny of the small protein with the CydA long Q-loop. Phylogenetic analysis suggests that the cydABX operon has undergone horizontal gene transfer, although the cydX gene likely evolved in a progenitor of the Alpha, Beta, and Gammaproteobacteria. Further investigation of cydAB operons identified two additional conserved hypothetical small proteins: CydY encoded in CydAQlong operons that lack cydX, and CydZ encoded in more than 150 CydAQshort operons.

Conclusions: This study provides a systematic analysis of bioinformatics techniques required for the unique challenges present in small protein identification and phylogenetic analyses. These results elucidate the prevalence of CydX throughout the Proteobacteria, provide insight into the selection pressure and sequence requirements for CydX function, and suggest a potential functional interaction between the small protein and the CydA Q-loop, an enigmatic domain of the cytochrome bd oxidase complex. Finally, these results identify other conserved small proteins encoded in cytochrome bd oxidase operons, suggesting that small protein subunits may be a more common component of these enzymes than previously thought.

Show MeSH
Related in: MedlinePlus