Genome Analyses of Three Strains of
            <i>Rhodobacter sphaeroides</i>
            : Evidence of Rapid Evolution of Chromosome II

Choudhary, Madhusudan; Zanhua, Xie; Fu, Yunxin; Kaplan, Samuel

doi:10.1128/jb.01498-06

Cited by 82 publications

(56 citation statements)

References 43 publications

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“…MC-1) showed no channel activity in previous studies (7). Of the bacteria containing the remaining 26 homologues, six of them were commercially available: B. licheniformis, isolated from soil and plant material (27), and L. vestfoldensis (28), R. sphaeroides (29), S. putrefaciens (30), R. denitrificans (31), and Oceanicaulis sp. (32) isolated from sea water (28 -33).…”

Section: Resultsmentioning

confidence: 99%

Comparative Study of the Gating Motif and C-type Inactivation in Prokaryotic Voltage-gated Sodium Channels

Irie

Kitagawa

Nagura

et al. 2010

Journal of Biological Chemistry

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Prokaryotic voltage-gated sodium channels (Na V s) are homotetramers and are thought to inactivate through a single mechanism, named C-type inactivation. Here we report the voltage dependence and inactivation rate of the NaChBac channel from Bacillus halodurans, the first identified prokaryotic Na V , as well as of three new homologues cloned from Bacillus licheniformis (Na V BacL), Shewanella putrefaciens (Na V SheP), and Roseobacter denitrificans (Na V RosD). We found that, although activated by a lower membrane potential, Na V BacL inactivates as slowly as NaChBac. Na V SheP and Na V RosD inactivate faster than NaChBac. Mutational analysis of helix S6 showed that residues corresponding to the "glycine hinge" and "PXP motif" in voltage-gated potassium channels are not obligatory for channel gating in these prokaryotic Na V s, but mutations in the regions changed the inactivation rates. Mutation of the region corresponding to the glycine hinge in Na V BacL (A214G), Na V SheP (A216G), and NaChBac (G219A) accelerated inactivation in these channels, whereas mutation of glycine to alanine in the lower part of helix S6 in NaChBac (G229A), Na V BacL (G224A), and Na V RosD (G217A) reduced the inactivation rate. These results imply that activation gating in prokaryotic Na V s does not require gating motifs and that the residues of helix S6 affect C-type inactivation rates in these channels.Voltage-gated sodium channels (Na V s) 3 generate the rapid upstroke of action potentials in nerve cell axons (1). In mammalian Na V s, the channel is formed by the ␣-subunit, which comprises four repeats of six-transmembrane segments, with each repeat consisting of 300 -400 amino acids. The ␣-subunit carries several glycosylation sites and co-assembles with auxiliary subunits to form the native channel (2, 3). The only structural information on Na V s available to date is a density map of the Na V from the electric organ of the electric eel determined by cryoelectron microscopy (4). Due to its limited resolution of 19 Å, the density map did not provide insights into the gating or sodium selectivity.The first prokaryotic Na V , NaChBac, was cloned from Bacillus halodurans (5). Subsequently, three more prokaryotic sodium channels were cloned and characterized (6, 7). All studied prokaryotic Na V s form homotetramers with a structure thought to be similar to that of some potassium channels with known structures (8 -10). Furthermore, because the proteins could be expressed in large amounts in Escherichia coli and purified by metal chelate affinity chromatography (5, 7, 11), they are promising candidates for high resolution structure determination and structure-function analyses.The physiological role of prokaryotic Na V s may be related to pH homeostasis, motility, and chemotaxis (6, 12). Searching bacterial genomic data bases, we found 26 sequences of putative NaChBac homologues from bacteria living in various environments. We were able to clone the putative Na V genes from three of these bacteria, Bacillus licheniformis, Shewanella pu...

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Section: Resultsmentioning

confidence: 99%

Comparative Study of the Gating Motif and C-type Inactivation in Prokaryotic Voltage-gated Sodium Channels

Irie

Kitagawa

Nagura

et al. 2010

Journal of Biological Chemistry

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“…Similar to Roseobacter, members of Rhodobacter are also metabolically versatile and exhibit genomic complexity (Nereng and Kaplan, 1999;Choudhary et al, 2004Choudhary et al, , 2007). …”

Section: Introductionmentioning

confidence: 99%

Gene transfer agent (GTA) genes reveal diverse and dynamic Roseobacter and Rhodobacter populations in the Chesapeake Bay

et al. 2008

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Within the bacterial class Alphaproteobacteria, the order Rhodobacterales contains the Roseobacter and Rhodobacter clades. Roseobacters are abundant and play important biogeochemical roles in marine environments. Roseobacter and Rhodobacter genomes contain a conserved gene transfer agent (GTA) gene cluster, and GTA-mediated gene transfer has been observed in these groups of bacteria. In this study, we investigated the genetic diversity of these two groups in Chesapeake Bay surface waters using a specific PCR primer set targeting the conserved Rhodobacterales GTA major capsid protein gene (g5). The g5 gene was successfully amplified from 26 Rhodobacterales isolates and the bay microbial communities using this primer set. Four g5 clone libraries were constructed from microbial assemblages representing different regions and seasons of the bay and yielded diverse sequences. In total, 12 distinct g5 clusters could be identified among 158 Chesapeake Bay clones, 11 fall within the Roseobacter clade, and one falls in the Rhodobacter clade. The vast majority of the clusters (10 out of 12) lack cultivated representatives. The composition of g5 sequences varied dramatically along the bay during the wintertime, and a distinct Roseobacter population composition between winter and summer was observed. The congruence between g5 and 16S rRNA gene phylogenies indicates that g5 may serve as a useful genetic marker to investigate diversity and abundance of Roseobacter and Rhodobacter in natural environments. The presence of the g5 gene in the natural populations of Roseobacter and Rhodobacter implies that genetic exchange through GTA transduction could be an important mechanism for maintaining the metabolic flexibility of these groups of bacteria.

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“…Comparative genome analysis shows that while the chromosome gene organization of WS8N is similar to that of previously sequenced strains of R. sphaeroides, the plasmid composition differs considerably, with ATCC_17029 having one, WS8N and KD131 each having two (6), and 2.4.1 and ATCC_17025 each having five (2).…”

mentioning

confidence: 58%

Genome Sequence of Rhodobacter sphaeroides Strain WS8N

et al. 2011

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Genome Analyses of Three Strains of Rhodobacter sphaeroides : Evidence of Rapid Evolution of Chromosome II

Cited by 82 publications

References 43 publications

Comparative Study of the Gating Motif and C-type Inactivation in Prokaryotic Voltage-gated Sodium Channels

Comparative Study of the Gating Motif and C-type Inactivation in Prokaryotic Voltage-gated Sodium Channels

Gene transfer agent (GTA) genes reveal diverse and dynamic Roseobacter and Rhodobacter populations in the Chesapeake Bay

Genome Sequence of Rhodobacter sphaeroides Strain WS8N

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