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Comparative genomics of transport proteins in developmental bacteria: Myxococcus xanthus and Streptomyces coelicolor.

Getsin I, Nalbandian GH, Yee DC, Vastermark A, Paparoditis PC, Reddy VS, Saier MH - BMC Microbiol. (2013)

Bottom Line: Except for electron transport carriers, there is a poor correlation between the types of transporters found in these two organisms, suggesting that their solutions to differentiative and metabolic needs evolved independently.A number of unexpected and surprising observations are presented, and predictions are made regarding the physiological functions of recognizable transporters as well as the existence of yet to be discovered transport systems in these two important model organisms and their relatives.The results provide insight into the evolutionary processes by which two dissimilar prokaryotes evolved complexity, particularly through selective chromosomal gene amplification.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA. msaier@ucsd.edu.

ABSTRACT

Background: Two of the largest fully sequenced prokaryotic genomes are those of the actinobacterium, Streptomyces coelicolor (Sco), and the δ-proteobacterium, Myxococcus xanthus (Mxa), both differentiating, sporulating, antibiotic producing, soil microbes. Although the genomes of Sco and Mxa are the same size (~9 Mbp), Sco has 10% more genes that are on average 10% smaller than those in Mxa.

Results: Surprisingly, Sco has 93% more identifiable transport proteins than Mxa. This is because Sco has amplified several specific types of its transport protein genes, while Mxa has done so to a much lesser extent. Amplification is substrate- and family-specific. For example, Sco but not Mxa has amplified its voltage-gated ion channels but not its aquaporins and mechano-sensitive channels. Sco but not Mxa has also amplified drug efflux pumps of the DHA2 Family of the Major Facilitator Superfamily (MFS) (49 versus 6), amino acid transporters of the APC Family (17 versus 2), ABC-type sugar transport proteins (85 versus 6), and organic anion transporters of several families. Sco has not amplified most other types of transporters. Mxa has selectively amplified one family of macrolid exporters relative to Sco (16 versus 1), consistent with the observation that Mxa makes more macrolids than does Sco.

Conclusions: Except for electron transport carriers, there is a poor correlation between the types of transporters found in these two organisms, suggesting that their solutions to differentiative and metabolic needs evolved independently. A number of unexpected and surprising observations are presented, and predictions are made regarding the physiological functions of recognizable transporters as well as the existence of yet to be discovered transport systems in these two important model organisms and their relatives. The results provide insight into the evolutionary processes by which two dissimilar prokaryotes evolved complexity, particularly through selective chromosomal gene amplification.

Show MeSH
Myxococcus xanthus transported substrate types. Types of substrates transported in Myxococcus xanthus by class a) and subclass b).
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Figure 5: Myxococcus xanthus transported substrate types. Types of substrates transported in Myxococcus xanthus by class a) and subclass b).

Mentions: Table 5 and Figure 5 show numbers of transport proteins in Sco organized according to substrate types. Transporters that utilize inorganic molecules as substrates make up a large portion of all transport proteins found in Mxa. Cation-specific transporters (23.7% -- 84 total) are split evenly between primary and secondary carrier systems (36 and 38 proteins, respectively) with only six recognized channels. There are markedly fewer inorganic anion transporters (5.1% -- 18 total), including 6 primary carriers and 10 secondary carriers. In comparison, there are relatively few electron transport systems in Mxa.


Comparative genomics of transport proteins in developmental bacteria: Myxococcus xanthus and Streptomyces coelicolor.

Getsin I, Nalbandian GH, Yee DC, Vastermark A, Paparoditis PC, Reddy VS, Saier MH - BMC Microbiol. (2013)

Myxococcus xanthus transported substrate types. Types of substrates transported in Myxococcus xanthus by class a) and subclass b).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3924187&req=5

Figure 5: Myxococcus xanthus transported substrate types. Types of substrates transported in Myxococcus xanthus by class a) and subclass b).
Mentions: Table 5 and Figure 5 show numbers of transport proteins in Sco organized according to substrate types. Transporters that utilize inorganic molecules as substrates make up a large portion of all transport proteins found in Mxa. Cation-specific transporters (23.7% -- 84 total) are split evenly between primary and secondary carrier systems (36 and 38 proteins, respectively) with only six recognized channels. There are markedly fewer inorganic anion transporters (5.1% -- 18 total), including 6 primary carriers and 10 secondary carriers. In comparison, there are relatively few electron transport systems in Mxa.

Bottom Line: Except for electron transport carriers, there is a poor correlation between the types of transporters found in these two organisms, suggesting that their solutions to differentiative and metabolic needs evolved independently.A number of unexpected and surprising observations are presented, and predictions are made regarding the physiological functions of recognizable transporters as well as the existence of yet to be discovered transport systems in these two important model organisms and their relatives.The results provide insight into the evolutionary processes by which two dissimilar prokaryotes evolved complexity, particularly through selective chromosomal gene amplification.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA. msaier@ucsd.edu.

ABSTRACT

Background: Two of the largest fully sequenced prokaryotic genomes are those of the actinobacterium, Streptomyces coelicolor (Sco), and the δ-proteobacterium, Myxococcus xanthus (Mxa), both differentiating, sporulating, antibiotic producing, soil microbes. Although the genomes of Sco and Mxa are the same size (~9 Mbp), Sco has 10% more genes that are on average 10% smaller than those in Mxa.

Results: Surprisingly, Sco has 93% more identifiable transport proteins than Mxa. This is because Sco has amplified several specific types of its transport protein genes, while Mxa has done so to a much lesser extent. Amplification is substrate- and family-specific. For example, Sco but not Mxa has amplified its voltage-gated ion channels but not its aquaporins and mechano-sensitive channels. Sco but not Mxa has also amplified drug efflux pumps of the DHA2 Family of the Major Facilitator Superfamily (MFS) (49 versus 6), amino acid transporters of the APC Family (17 versus 2), ABC-type sugar transport proteins (85 versus 6), and organic anion transporters of several families. Sco has not amplified most other types of transporters. Mxa has selectively amplified one family of macrolid exporters relative to Sco (16 versus 1), consistent with the observation that Mxa makes more macrolids than does Sco.

Conclusions: Except for electron transport carriers, there is a poor correlation between the types of transporters found in these two organisms, suggesting that their solutions to differentiative and metabolic needs evolved independently. A number of unexpected and surprising observations are presented, and predictions are made regarding the physiological functions of recognizable transporters as well as the existence of yet to be discovered transport systems in these two important model organisms and their relatives. The results provide insight into the evolutionary processes by which two dissimilar prokaryotes evolved complexity, particularly through selective chromosomal gene amplification.

Show MeSH